I think you're in the wrong forum for this discussion. Try dealdatabase.com for your Tivo hacking questions. The Tivo Community Forum, which is an offshoot of this forum, does not permit discussions regarding video extraction.
You didn't indicate which converter you're using to create your mpg files but I'll assume you're using tytompg since that's about the only one that works with HDTivo files at the moment (I haven't tried out the latest TySuite GUI yet). Tympegs are indeed mpeg2 files but they're anything but standard. The gaps between GOP headers in normal mpeg2 files are pretty standard at about 18 frames apiece. Ty files tend to be all over the map in this regard. There can be as few as 1 or 2 frames or well over 100.
There are lots of issues using standard programs to play them back on your PC as a result. Some work fine and others simply don't like them. I'm not familiar with VLC so I can't help you there. Try using a DVD codec such as PowerDVD or WinDVD. I think you'll find they work quite well for this purpose.