After some more investigation, I have found that BD Ripper cannot seem to copy the Dolby TrueHD audio tracks. I tried 3 different TrueHD movies, and on all of them, BD Ripper failed to create a TrueHD audio track, even though it identified the track as being TrueHD, and I clicked it, and I did NOT check the "Remove HD audio" box. Instead, there was only an AC3 track, and the HD Audio light on my receiver did NOT light up when playing the MKV files.
Interestingly, BD Ripper does copy DTS-HD tracks properly. Even though MediaInfo does not identify the audio track in the MKV file as "DTS-HD", I have found that the MKV file from BD Ripper does indeed have the DTS-HD track on it -- when I play it with MPC-HC (ffdshow set for passthru for all audio types), my receiver lights up the HD audio light and identifies the sound as DTS HD.
I also tried ripping some TrueHD blu-rays (Spiderman 3, Batman Begins) to MKV with AnyDVD HD combined with Another EAC3to GUI. That combination correctly ripped the TrueHD audio track without difficulty. MediaInfo lists the audio track as TrueHD, and the HD Audio light on my receiver lights up when I play the MKV file.
So, bottom line is that my HTPC system is functioning correctly, but BD Ripper has a bug that it does not properly copy any Dolby TrueHD audio tracks to MKV files.
By the way, how often do the developers check these forums? When can I expect a response on this issue?