I have seen the same flicker with the resolution set to 720... changed back to 544 and it went away again. Sorry I missed your original post or I would have suggested checking the resolution setting!
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To clarify, the TiVo had two issues, intermittent horizontal green lines, and then the inverted image flicker at the bottom of the screen.
The green lines were fixed by replacing the SAA7114H chip, and the image flicker at the bottom of the screen was fixed by setting the resolution from 720 back to 544.