Yeah I ran into this problem. If I use Goto or try to change the Audio track the PlayOn starts to play the MKV H.264 at 2x speed with no audio.
This is definitely down the Variable Frame Rate. If I encode the same movie with exactly the same Handbrake settings but use --cfr then it works fine in the PlayOn.
So whos bug is this? PlayOn or Handbrake? I don't know. I need to do some research into if Variable Frame Rate on a H.264 in an MKV is legal. Everything else plays variable frame rate H.264 in a MKV container.
There is no way I am spending time mucking around re-encoding stuff just for the PlayOn. Who knows in 3 months the PlayOn may support VFR, or may even stop playing CFR. All media player manufacturers mess the users around with what is supported and what isn't, then blame encoders.
My solution which seems to work pretty well is to pause the film, select the audio track you want, press pause again, wait a couple of secs and then press play. If this doesn't work try again. Pause, pause, wait 2 secs, play. Its a bit of a hassle but its not like you constantly change audio in a movie.
This will have to do until I replace the PlayOn Mini. For me its pretty much an obsolete device. The r5440 firmware was horrendous. Slow, crashes and doesn't seem to even recognise subtitles in an MKV container. I went back to r3582 which is far from perfect.
At least these devices are relatively cheap so can be replaced frequently when they disappoint, which they frequently do. One day someone will manufacture a device with a decent quick interface that plays all codecs. That company will clean up.