if they are 1080p files with a high bitrate or are files without an AC3 track they will not play on older iDevices. If you are using the ATV3 HB setting you should have 2 audio tracks, so I'm assuming it would be the high bitrate.
You will be able to play any of your files if you either use the ATV2 preset, or if you lower the bitrate of your files. You can do this either by adjusting the CQ slider if you use that, or by lowering the bitrate amount if you do Variable Bit Rate encodes.