Cannot properly split/extract video, no matter what method I try.. please help!

[delus10n0]

I'm not a newbie at this, but I seem to be having nothing but 
problems. TivoApp doesn't work properly for me (bombs out halfway 
through most streams), and I have followed the directions in this 
method:

http://www.30below.com/~zmerch/tivo/index.cfm

And it works, but when I do a splitstream/zss on the TYstream, i end 
up with the "Bad" file containing over half the stream! For example:

smallville1.ty (original TyStream) - 2.6 gigs
smallville1.m2v (converted mpeg2 video) - 721 megs
smallville1.m2a (converted mpeg2 audio) - 23 megs
bad-smallville1.ty ("bad" tystream frames) - 1.9 gigs

It doesn't just happen with this particular TyStream, but with any I 
try and extract. My TiVO is recording in "BEST" quality, and VBR 
("Save Disk Space") is off. I am stumped, and cannot figure out for 
the life of me how anyone else out there is able to do this :) My 
TiVO software is still at 2.5 (hasn't jumped to 3.0 yet)

Does anyone have any advice or ideas to help me out? I'd really 
appreciate it. Thanks in advance!