I have a TiVo Series3 and something that has always bugged me is how the "native" resolution modes cause the screen to flick as it hops from 720p to 1080i for channel surfing or even jumping to the TiVo menu.
There are some settings for upconverting all HD content to 1080i, upconverting all SD and HD content to 1080i, etc.
I am concerned that the scaler in the TiVo is probably a lousy one and using "native" is the only way to preserve picture quality. TV is a Samsung HL50A650 DLP.
Marantz AVR & monoblocks + MartinLogan Motion 3.1 setup