Update:
Well, I found out that tivo.net won't work on Windows 2000, so that's not an option for me.
I downloaded videora and tried a few .avi files with that and had about the same luck as with the current converter I'm using Video Convert Master, but. . .
The settings that I was using on VCM were:
Bitrate 9000 kbps, audio 320kbps, sample rate 44000khz, aspect ratio Automatic, output .mpg2.
There are no settings in VCM for framerate, but even if I convert something like weeds with a 22 or 23 fps, it had always worked in the past.
I was thinking this was a video bitrate issue, since the audio was working, but after working with videora for a while, seeing that the video/audio settings were max 8192 and 192, I did various video bitrate settings, none worked with VCM.
Anyway, long story short(er), the only other option I had left (still not thinking it's audio since the audio is coming through) I changed the aspect ratio from automatic (in VCM) to 4:3.
Presto, it worked. 9000kbps, 4:3 aspect, same output file, still no framerate specification, so I don't know what it's outputting, but I would assume 29.xx as normal.
At the same time, I did decrease the audio bitrate to 192, so it could be both, or one or the other. I'll mess with it some more this weekend, see if when I put the audio back to 320 if it messes up, but I don't think it will.
It was such a minor change, that I'm not 100% sure it's the 'real' solution, but I'll keep ya'll updated on what I find.
p.s. it seems that the only files I download are .avi files, I get a few .mpg files, and in the past they have worked fine, but .avi is all I seem to get, so it's all I have experience with.