Not sure if others will be able to reproduce this. I actually need to do more to try and reproduce it. I think it occurs immediately after the first comskip marker. Basically the show is playing, then it skips through the first commercial marker, and now if I try to use the Left Arrow or Right Arrow to jump forward or back, nothing happens- the show continues to play without jumping forward/back. Doesn't matter how many times I press the L/R Arrow, the show won't skip forward/back.
It's not a Harmony remote issue because when it happens I can grab the GF's standard remote and won't work either. Also, I can see the little red LED on the IR receiver flickering when I am pressing the buttons, so the PC is getting the signal.
So far I have tried the Pause button, which still works, but after coming out of pause, the L/R Arrow buttons still don't work. The L/R Arrow buttons won't work until I press STOP, then play, then they will be working for the rest of the show. Or if I press STOP, I can then navigate around in Theaterview and the L/R Arrow buttons work just fine.
And the L/R Arrow buttons keep working until I play another show and get through that first commercial marker, where they (may) stop working again. I guess next time it happens, I will try other buttons like FF/REW or or Up/Down or Back or Guide etc.