I think I may have spotted a potential fix for your original wiring arrangement. I'm assuming that by "second set of outputs" you mean the second zone. If that is the case, then you need to make sure of a few things before you start recording.

1. Make sure the second zone is turned on and set to the correct input (video1 for the Tivo).
2. Make sure the device being recorded has a set of analog audio cables and a video cable that is the same type as the second zone output is using (in other words, if the DVD-R is connected to the s-video output, then you will want to connect an s-video cable from the Tivo to the 990). This is because zone 2 is a purely analog pre-amp with video switching but no video conversion between composite and s-video.
3. Make sure you have the second zone volume set to a level that works well with your recordings (probably somewhat on the high side).

If you do those things, you should be able to get video from the active second zone input to the DVD-R.