Same problem here: MKV file with embedded subtitles. Running Finless Bobs ROM 2.1 on an MK808.
When I play the file from a local directory, no problem, all subtitles are shown independent of HW or HW+ mode. When I try to play the SAME file from my NAS drive (accessing it with ES file explorer), the embedded subtitles do not show up, as if they were not existing.
The HW+ workaround above does work, but is not a satisfactory solution: Switching to HW+ does make the subtitles appear and selectable, video plays but stutters. You can then switch back to HW with the subtitles on, video plays smooth but freezes after ~5 seconds. So no working solution for NAS.
Hope this helps to reproduce the issue - please fix it!