Originally Posted by Goes to 11
A problem has developed.
In addition to the previous suggestions...
1. Try different stations in case it is some kind of encoding or AV interleave issues. The TV station may have changed their encoding. There is one station I get that takes up to 20 seconds for me to get a clear signal which I think is due to the way they encode (key frames being 20 seconds apart). This could be why when it changes channels on a programmed record you see the problem but not on a manual recording. Of course you would experience this changing channels as well.
2. Try your strongest station.
3. Try changing your audio output to All Analog (just to see if you can otherwise hear the audio in the places with missing audio). I use a digital TOSLINK feed to my home theatre, weak signals cause the receiver to occasionally drop out if there is a problem in the signal but the analog audio doesn't drop out. I interpret this as the TVIX is better at handling the digital audio than my receiver. Instead of changing the audio to analog you could try using the audio RCA jacks.
4. It could actually be the harddrive. I normally say advise people that defragging is a waste of time but I can see with my TVIX that for a second or two on new recordings, it can occasionally be jittery. But this lasts only a second or two. I blame the HD for this. You're on the right track trying a different drive.
Run MediaInfo on the files you recorded to see details of what the TV station is broadcasting.