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I forgot to mention that the subtitles are .PGS format. I started with an .M2TS file and converted to mkv that has the pgs subtitles in it.
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The obvious answer is to extract them from the M2TS or MKV file and add them in separately. Apparently both Handbrake and VidCoder accept Blu-Ray subs as input. I wouldn't know for sure because I don't use those programs. Try MKVExtract or maybe BDSup2SUB.
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From https://trac.handbrake.fr/wiki/Subtitles
With MP4, you can burn ONLY 1 subtitle track into the video. You can not pass-through PGS into MP4 as this file format does not support it
So you can use the burn-in or convert PGS to IDX/SUB (BDSup2Sub) and mux those in (MyMP4Box GUI) or you could perform OCR of the PGS to ttxt (Subtitle Edit) and mux those.
But why re-encode the m2ts? You could re-mux the .m2ts to .ts (tsMuxeR GUI) and use that in My MP4Box GUI together with idx/sub or has it to be h.264 video? -
I have an update and a different problem. I have successfully created an srt file that I muxed into the mkv with mkvtoolnix. When I play the movie with vlc, the subtitles are there. The frustrating problem, and for the life of me, I cannot get this sort into an mp4 and have the subtitles play. I tried the following: Using vidcoder to convert the mov to mp4 and selecting the srt from the source. I also loaded the mkv and then imported the .srt separately. I read somewhere to used subedit to convert the srt to ssa then mux the ssa with the mkv. I also tried muxing the mp4 and .srt with mp4boxgui. NONE OF THESE WORKED. I did notice something consistent with everything I tried. In the .mkv file, MediaInfo shows the subtitle as a UTF-8 file ID: 3. In the .mp4, it is showing it as a Timed Text and the codec ID is tx3g and is not retaining the UTF-8.
One other thing: when the .mp4 and .srt are in the same folder, the .mp4 plays the subtitle. Not sure if this is a factor, but I can't imagine it being this difficult when I've come this far with the information I provided above. Please help!!