It sounds exactly like a codec problem to me. Without knowing what model of TiVo you have and what operating system your PC is running I can't be sure, but my best guess is that you don't have an AC3 codec or the one you do have doesn't work right. Try AC3Filter.
If you still have problems after that, go to the Home Media forum here and try the codec utility in the sticky at the top of the page. Open one of the files in question with it and post a screenshot of the filter graph it shows. It would also help if you download MediaInfo, switch to the text view, and post the detailed info on one of the recordings.
The recording that was delayed due to the Olympics probably switched to a different audio encoding method when ET came on.