I just installed Channels DVR yesterday. After trying two recordings with commercial detection enabled, I had to turn the NAS off and on both times because it had become completely unresponsive. I have both a HDHomeRun Prime and Extend. It was recording from the Prime. Just now I recorded a show with commercial detection turned off and had no problems with either recording or viewing.
I also use Plex with commercial detection/removal on the PR2100 and that does not seem to cause any problems. It looks like the Channels commercial detection code needs more work, at least for the PR2100. I am going to leave it turned off for now.
Otherwise I really like the Channels software. The user interface is much better than I have seen on other applications.