I tried doing what you said Shark, and disabled the LAV filter, and unfortunately still had the same problem. It seems strange, but sometimes when I reboot, the quietness isn't anywhere near as bad. I only have to raise the volume half of what I usually do to get the sound (but it still needs raising).
I was also wondering could it be to do with the file using surround sound? I am only playing through TV speakers, and I know at least one of the programs is usually surround sound (however, all sound is quiet, as opposed to just voice. If it was a surround sound issue, I'd expect to hear loud music/effects, and low voice). However, when I watch the same thing on an xvid rip, there are no issues.
I've noticed that sometimes the avi files need to be louder than the volume for live tv in WMC. It all appears to be very random.
Any other ideas?
I just noticed in the Shark codec settings that 'disable auto speaker configuration' wasn't checked. I checked it, and selected 2.0 stereo. It is no longer as bad, but still requires significantly higher volume on the TV than other files.