Posting an activity log from handbrake would help. Also, have you checked that the MKV file doesn't have the same audio drop?
[10:46:46] hb_init: checking cpu count
[10:46:46] hb_init: starting libhb thread
[10:46:46] macgui: Handbrake Version: 0.9.5 x86_64 (2011010300)
[10:46:46] hb_init: checking cpu count
[10:46:46] hb_init: starting libhb thread
[10:46:46] hb_init: checking cpu count
[10:46:46] hb_init: starting libhb thread
[10:46:46] macgui: hbInstances path to this instance: /Applications/HandBrake.app
[10:46:46] macgui: hbInstance found instance pidnum:2419 at path: /Applications/HandBrake.app
[10:46:46] macgui: hbInstance MATCH FOUND, our pidnum is:2419
[10:46:46] macgui: Pid for this instance:2419
[10:46:46] macgui: HBQueueController : My Pidnum is 2419
[10:46:49] macgui: didDimissReloadQueue number of hb instances:1
[10:46:49] macgui: didDimissReloadQueue NSAlertOtherReturn Chosen
[10:47:06] macgui: trying to open video_ts folder (parent directory chosen)
[10:47:06] macgui: Preview: Disabling HUD Controls
[10:47:06] macgui: Minimum length of title for scan: 900000
[10:47:06] hb_scan: path=/Users/XXXXXXXX/Movies/Taken/t00_Taken.mkv, title_index=0
libbluray/bdnav/index_parse.c:157: indx_parse(): error opening /Users/XXXXXXXXXX/Movies/Taken/t00_Taken.mkv/BDMV/index.bdmv
libbluray/bluray.c:960: nav_get_title_list(/Users/XXXXXXXXXX/Movies/Taken/t00_Taken.mkv) failed (0x10212ee00)
[10:47:06] bd: not a bd - trying as a stream/file instead
libdvdnav: Using dvdnav version 4.1.3
libdvdread: Using libdvdcss version 1.2.10 for DVD access
libdvdnav

VDOpenFileUDF:UDFFindFile /VIDEO_TS/VIDEO_TS.IFO failed
libdvdnav

VDOpenFileUDF:UDFFindFile /VIDEO_TS/VIDEO_TS.BUP failed
libdvdread: Can't open file VIDEO_TS.IFO.
libdvdnav: vm: failed to read VIDEO_TS.IFO
[10:47:06] dvd: not a dvd - trying as a stream/file instead
Input #0, matroska,webm, from '/Users/XXXXXXXX/Movies/Taken/t00_Taken.mkv':
Metadata:
title : Taken
Duration: 01:30:55.19, start: 0.000000, bitrate: 1536 kb/s
Chapter #0.0: start 0.000000, end 283.950333
Metadata:
title : Chapter 00
Chapter #0.1: start 283.950333, end 476.017200
Metadata:
title : Chapter 01
Chapter #0.2: start 476.017200, end 772.605156
Metadata:
title : Chapter 02
Chapter #0.3: start 772.605156, end 1006.171800
Metadata:
title : Chapter 03
Chapter #0.4: start 1006.171800, end 1221.303378
Metadata:
title : Chapter 04
Chapter #0.5: start 1221.303378, end 1455.745889
Metadata:
title : Chapter 05
Chapter #0.6: start 1455.745889, end 1727.851067
Metadata:
title : Chapter 06
Chapter #0.7: start 1727.851067, end 1923.004356
Metadata:
title : Chapter 07
Chapter #0.8: start 1923.004356, end 2130.044533
Metadata:
title : Chapter 08
Chapter #0.9: start 2130.044533, end 2311.851156
Metadata:
title : Chapter 09
Chapter #0.10: start 2311.851156, end 2471.010156
Metadata:
title : Chapter 10
Chapter #0.11: start 2471.010156, end 2724.263156
Metadata:
title : Chapter 11
Chapter #0.12: start 2724.263156, end 3060.140333
Metadata:
title : Chapter 12
Chapter #0.13: start 3060.140333, end 3318.857133
Metadata:
title : Chapter 13
Chapter #0.14: start 3318.857133, end 3414.911422
Metadata:
title : Chapter 14
Chapter #0.15: start 3414.911422, end 3769.265400
Metadata:
title : Chapter 15
Chapter #0.16: start 3769.265400, end 3925.046044
Metadata:
title : Chapter 16
Chapter #0.17: start 3925.046044, end 4128.123911
Metadata:
title : Chapter 17
Chapter #0.18: start 4128.123911, end 4403.774267
Metadata:
title : Chapter 18
Chapter #0.19: start 4403.774267, end 4585.872867
Metadata:
title : Chapter 19
Chapter #0.20: start 4585.872867, end 4760.922733
Metadata:
title : Chapter 20
Chapter #0.21: start 4760.922733, end 5012.882778
Metadata:
title : Chapter 21
Chapter #0.22: start 5012.882778, end 5136.339444
Metadata:
title : Chapter 22
Chapter #0.23: start 5136.339444, end 5455.199000
Metadata:
title : Chapter 23
Stream #0.0(eng): Video: h264, yuv420p, 1920x1080 [PAR 1:1 DAR 16:9], 23.98 fps, 24 tbr, 1k tbn, 47.95 tbc
Stream #0.1(eng): Audio: dca, 48000 Hz, 5.1, s16, 1536 kb/s
Metadata:
title : 3/2+1
[10:47:07] scan: decoding previews for title 1
[10:47:07] scan: audio 0x1: DCA, rate=48000Hz, bitrate=1536000 English (DTS) (5.1 ch)
[10:47:09] scan: 10 previews, 1920x1080, 23.976 fps, autocrop = 0/0/0/0, aspect 16:9, PAR 1:1
[10:47:09] scan: title (0) job->width:1920, job->height:1072
[10:47:09] libhb: scan thread found 1 valid title(s)
[10:47:09] macgui: showNewScan: This is a new source item scan
[10:47:09] macgui: Preview: Enabling HUD Controls
[10:48:39] macgui: Rip: Pending queue count is 0
[10:48:39] macgui: getNextPendingQueueIndex next pending encode index is:0
[10:48:39] macgui: scanning specifically for title: 1
[10:48:39] hb_scan: path=/Users/XXXXXXXXX/Movies/Taken/t00_Taken.mkv, title_index=1
libbluray/bdnav/index_parse.c:157: indx_parse(): error opening /Users/XXXXXXXXXX/Movies/Taken/t00_Taken.mkv/BDMV/index.bdmv
libbluray/bluray.c:960: nav_get_title_list(/Users/XXXXXXXXX/Movies/Taken/t00_Taken.mkv) failed (0x103109400)
[10:48:39] bd: not a bd - trying as a stream/file instead
libdvdnav: Using dvdnav version 4.1.3
libdvdread: Using libdvdcss version 1.2.10 for DVD access
libdvdnav

VDOpenFileUDF:UDFFindFile /VIDEO_TS/VIDEO_TS.IFO failed
libdvdnav

VDOpenFileUDF:UDFFindFile /VIDEO_TS/VIDEO_TS.BUP failed
libdvdread: Can't open file VIDEO_TS.IFO.
libdvdnav: vm: failed to read VIDEO_TS.IFO
[10:48:39] dvd: not a dvd - trying as a stream/file instead
Input #0, matroska,webm, from '/Users/XXXXXXXXXX/Movies/Taken/t00_Taken.mkv':
Metadata:
title : Taken
Duration: 01:30:55.19, start: 0.000000, bitrate: 1536 kb/s
Chapter #0.0: start 0.000000, end 283.950333
Metadata:
title : Chapter 00
Chapter #0.1: start 283.950333, end 476.017200
Metadata:
title : Chapter 01
Chapter #0.2: start 476.017200, end 772.605156
Metadata:
title : Chapter 02
Chapter #0.3: start 772.605156, end 1006.171800
Metadata:
title : Chapter 03
Chapter #0.4: start 1006.171800, end 1221.303378
Metadata:
title : Chapter 04
Chapter #0.5: start 1221.303378, end 1455.745889
Metadata:
title : Chapter 05
Chapter #0.6: start 1455.745889, end 1727.851067
Metadata:
title : Chapter 06
Chapter #0.7: start 1727.851067, end 1923.004356
Metadata:
title : Chapter 07
Chapter #0.8: start 1923.004356, end 2130.044533
Metadata:
title : Chapter 08
Chapter #0.9: start 2130.044533, end 2311.851156
Metadata:
title : Chapter 09
Chapter #0.10: start 2311.851156, end 2471.010156
Metadata:
title : Chapter 10
Chapter #0.11: start 2471.010156, end 2724.263156
Metadata:
title : Chapter 11
Chapter #0.12: start 2724.263156, end 3060.140333
Metadata:
title : Chapter 12
Chapter #0.13: start 3060.140333, end 3318.857133
Metadata:
title : Chapter 13
Chapter #0.14: start 3318.857133, end 3414.911422
Metadata:
title : Chapter 14
Chapter #0.15: start 3414.911422, end 3769.265400
Metadata:
title : Chapter 15
Chapter #0.16: start 3769.265400, end 3925.046044
Metadata:
title : Chapter 16
Chapter #0.17: start 3925.046044, end 4128.123911
Metadata:
title : Chapter 17
Chapter #0.18: start 4128.123911, end 4403.774267
Metadata:
title : Chapter 18
Chapter #0.19: start 4403.774267, end 4585.872867
Metadata:
title : Chapter 19
Chapter #0.20: start 4585.872867, end 4760.922733
Metadata:
title : Chapter 20
Chapter #0.21: start 4760.922733, end 5012.882778
Metadata:
title : Chapter 21
Chapter #0.22: start 5012.882778, end 5136.339444
Metadata:
title : Chapter 22
Chapter #0.23: start 5136.339444, end 5455.199000
Metadata:
title : Chapter 23
Stream #0.0(eng): Video: h264, yuv420p, 1920x1080 [PAR 1:1 DAR 16:9], 23.98 fps, 24 tbr, 1k tbn, 47.95 tbc
Stream #0.1(eng): Audio: dca, 48000 Hz, 5.1, s16, 1536 kb/s
Metadata:
title : 3/2+1
[10:48:39] scan: decoding previews for title 1
[10:48:39] scan: audio 0x1: DCA, rate=48000Hz, bitrate=1536000 English (DTS) (5.1 ch)
[10:48:41] scan: 10 previews, 1920x1080, 23.976 fps, autocrop = 0/0/0/0, aspect 16:9, PAR 1:1
[10:48:41] scan: title (0) job->width:1920, job->height:1072
[10:48:41] libhb: scan thread found 1 valid title(s)
[10:48:42] macgui: ScanDone state received from fQueueEncodeLibhb
[10:48:42] macgui: Preset: Custom
[10:48:42] macgui: processNewQueueEncode number of passes expected is: 1
[10:48:42] macgui: Start / Stop set to chapters
[10:48:42] macgui: prepareJob exiting
[10:48:42] 1 job(s) to process
[10:48:42] starting job
[10:48:42] sync: expecting 130818 video frames
[10:48:42] job configuration:
[10:48:42] * source
[10:48:42] + /Users/XXXXXXXXXX/Movies/Taken/t00_Taken.mkv
[10:48:42] + title 1, chapter(s) 1 to 24
[10:48:42] + container: matroska,webm
[10:48:42] + data rate: 1536 kbps
[10:48:42] * destination
[10:48:42] + /Users/XXXXXXXXXX/Desktop/t00_Taken.m4v
[10:48:42] + container: MPEG-4 (.mp4 and .m4v)
[10:48:42] + 64-bit formatting
[10:48:42] + chapter markers
[10:48:42] * video track
[10:48:42] + decoder: h264
[10:48:42] + frame rate: 23.976 fps -> peak rate limited to 29.970 fps
[10:48:42] + loose anamorphic
[10:48:42] + storage dimensions: 1920 * 1080 -> 1280 * 720, crop 0/0/0/0, mod 16
[10:48:42] + pixel aspect ratio: 1 / 1
[10:48:42] + display dimensions: 1280 * 720
[10:48:42] + encoder: x264
[10:48:42] + quality: 18.50 (RF)
[10:48:42] * audio track 0
[10:48:42] + decoder: English (DTS) (5.1 ch) (track 1, id 1)
[10:48:42] + bitrate: 1536 kbps, samplerate: 48000 Hz
[10:48:42] + mixdown: Dolby Pro Logic II
[10:48:42] + encoder: ca_aac
[10:48:42] + bitrate: 160 kbps, samplerate: 48000 Hz
[10:48:42] * audio track 1
[10:48:42] + decoder: English (DTS) (5.1 ch) (track 1, id 1)
[10:48:42] + bitrate: 1536 kbps, samplerate: 48000 Hz
[10:48:42] + mixdown: 6-channel discrete
[10:48:42] + encoder: ffac3
[10:48:42] + bitrate: 640 kbps, samplerate: 48000 Hz
[10:48:42] encx264: min-keyint: auto (29), keyint: 300
[10:48:42] encx264: encoding with stored aspect 1/1
[10:48:42] encx264: Encoding at constant RF 18.500000
x264 [info]: using SAR=1/1
x264 [info]: using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.2
x264 [info]: profile High, level 3.1
[10:48:42] reader: first SCR 0 id 0 DTS 0
Stream with high frequencies VQ coding
Stream with high frequencies VQ coding
[10:54:49] h264: "Chapter 01" (2) at frame 6818 time 25563060
[10:59:41] h264: "Chapter 02" (3) at frame 11422 time 42845310
[11:07:33] h264: "Chapter 03" (4) at frame 18533 time 69538230
[11:13:30] h264: "Chapter 04" (5) at frame 24132 time 90555480
[11:19:24] h264: "Chapter 05" (6) at frame 29291 time 109921050
[11:25:00] h264: "Chapter 06" (7) at frame 34911 time 131017140
[11:30:14] h264: "Chapter 07" (8) at frame 41436 time 155510370
[11:34:12] h264: "Chapter 08" (9) at frame 46115 time 173074140
[11:38:52] h264: "Chapter 09" (10) at frame 51078 time 191704050
[11:42:51] h264: "Chapter 10" (11) at frame 55439 time 208074150
[11:46:30] h264: "Chapter 11" (12) at frame 59254 time 222394680
[11:53:03] h264: "Chapter 12" (13) at frame 65326 time 245187450
[12:00:10] h264: "Chapter 13" (14) at frame 73380 time 275420160
[12:05:33] h264: "Chapter 14" (15) at frame 79582 time 298700910
[12:07:31] h264: "Chapter 15" (16) at frame 81884 time 307342080
[12:14:49] h264: "Chapter 16" (17) at frame 90380 time 339233940
[12:17:34] h264: "Chapter 17" (18) at frame 94116 time 353257920
[12:21:50] h264: "Chapter 18" (19) at frame 98984 time 371531160
[12:27:27] h264: "Chapter 19" (20) at frame 105595 time 396347220
[12:30:53] h264: "Chapter 20" (21) at frame 109959 time 412728570
[12:35:08] h264: "Chapter 21" (22) at frame 114157 time 428486850
[12:40:40] h264: "Chapter 22" (23) at frame 120197 time 451159470
[12:43:25] h264: "Chapter 23" (24) at frame 123158 time 462274290
[12:46:57] reader: done. 1 scr changes
[12:46:58] work: average encoding speed for job is 18.429775 fps
[12:46:59] sync: got 130794 frames, 130818 expected
[12:46:59] h264-decoder done: 130794 frames, 0 decoder errors, 0 drops
[12:46:59] render: 130794 frames output, 0 dropped and 0 duped for CFR/PFR
[12:46:59] render: lost time: 0 (0 frames)
[12:46:59] render: gained time: 0 (0 frames) (0 not accounted for)
x264 [info]: frame I:2970 Avg QP:14.97 size: 87241 PSNR Mean Y:46.95 U:50.10 V:51.21 Avg:47.83 Global:47.35
x264 [info]: frame P:69362 Avg QP:20.40 size: 29697 PSNR Mean Y:44.63 U:48.49 V:49.80 Avg:45.64 Global:44.96
x264 [info]: frame B:58462 Avg QP:22.23 size: 13527 PSNR Mean Y:43.84 U:48.57 V:49.40 Avg:44.91 Global:44.06
x264 [info]: consecutive B-frames: 24.8% 39.8% 8.4% 27.0%
x264 [info]: mb I I16..4: 25.1% 63.9% 11.0%
x264 [info]: mb P I16..4: 2.1% 9.1% 1.0% P16..4: 31.0% 15.9% 8.7% 0.0% 0.0% skip:32.1%
x264 [info]: mb B I16..4: 0.1% 1.4% 0.1% B16..8: 37.3% 5.9% 1.4% direct: 3.6% skip:50.2% L0:44.0% L1:49.1% BI: 6.9%
x264 [info]: 8x8 transform intra:73.1% inter:65.5%
x264 [info]: coded y,uvDC,uvAC intra: 73.1% 77.8% 52.3% inter: 26.7% 26.2% 3.7%
x264 [info]: i16 v,h,dc,p: 68% 11% 7% 14%
x264 [info]: i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 13% 13% 32% 6% 7% 7% 7% 7% 9%
x264 [info]: i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 19% 16% 18% 7% 9% 9% 8% 7% 6%
x264 [info]: i8c dc,h,v,p: 57% 18% 18% 7%
x264 [info]: Weighted P-Frames: Y:2.2% UV:1.0%
x264 [info]: ref P L0: 58.6% 12.0% 19.9% 9.2% 0.2%
x264 [info]: ref B L0: 78.6% 19.2% 2.1%
x264 [info]: ref B L1: 95.6% 4.4%
x264 [info]: SSIM Mean Y:0.9735624 (15.778db)
x264 [info]: PSNR Mean Y:44.331 U:48.562 V:49.654 Avg:45.364 Global:44.574 kb/s:4560.46
[12:46:59] mux: track 0, 130794 frames, 3109699273 bytes, 4560.33 kbps, fifo 8
[12:46:59] mux: track 1, 255714 frames, 111685560 bytes, 163.79 kbps, fifo 512
[12:46:59] mux: track 2, 170475 frames, 436416000 bytes, 640.00 kbps, fifo 256
[12:46:59] libhb: work result = 0
[12:46:59] macgui: incrementQueueItemDone there are no more pending encodes