So, after a week of nothing but good results, I've stumbled upon a recording that still gives me the problem.
This particular capture, the audio cuts halfway through the show.
Here's a log from ProjectX
http://pastebin.com/yqpaV2AC
Anyway, I messed with ProjectX options and, on the Audio tab, I found an option to convert the audio while demultiplexing to MPEG1. I did that and, apparently, it fixed my issue: On the next audio pass, the audio was there entirely.
I hope that fixes it for good!
Once again, thanks for all the help.