I have a similar setup to yours, and it sounds to me like you've covered all the bases. In re-reading your post, I can only puzzle over the following:
1. You've changed both "Bitrates" and "Alt Bitrates"?
2. You're changing the for the correct input (e.g. CATV or Sat or Antenna etc.)?
3. Your Quality settings are all different (mine are 0, 40, 75, and 100, the 40 being for Medium which is where my own SVCD settings are done)?
I'm not sure what else to suggest; it sounds like you've done everything else right. I can't even imagine that Tivoweb is at issue as to my knowledge its Resource Editor just reads the actual settings out of the Tivo.
My own SVCD settings (I use the Medium settintgs) are 2 (480x480), VBR of 2000 (don't care; Save Disk is OFF), MAX is 2760 (2760-160=2600 CBR for video), and Quality is 40.
Philips Standalone v3.01 w/2-80G drives and Tivonet.