I only have memory to go on as all of my material is ripped, but if I recall correctly, I only had the forced subtitles check from the MakeMKV scan, and still select the "Foreign Audio Search". I would suggest going to the Handbrake forum for good expertise on this. I will check a few things on my files, but that's about as far as I can take you, right now.
Edit: I am going to correct what I said. When I rip with MakeMKV, I save all English subtitles (forced and non-forced) as I am creating a duplicate of the disc so I can go back to it, if needed.
Update: I thought you might be interested in this from the HB Forum:
Re: PGS Subtitles
by kfreeb » Sun May 13, 2012 2:57 pm
I have just re-ripped Avatar, using MakeMKV and extracted only the forced subtitle track, (english) and re-encoded it with handbrake, (with only burn-in selected in the Subtitle menu of HB, forced sub unchecked) the subtitles stay on screen for very long periods of time, till the next forced subtitle comes along, never clears off.
So it seems that it is something going on with MakeMKV that you are selecting only forced subs but it is not creating a subtitle track for HB to work from.