What modern firmware are people using? Are there any active (heck, semi-active) groups still releasing updates?
MKV encoded files using Handbrake save subtitle streams as "S_HDMV/PGS". These play as expected using VLC and other playback software on my computer.
The only workarounds I've found is to either download srt files (hoping they are correct) or demux the video and hand edit them with SupRip (time consuming, but correct).
I'm now running AMP_r9_pohd (ACRBO firmware PV73100_v7.4.x.r7317) and there's no difference with subtitles.