I had two problems. One is solved.

1) The VCR record return does not transpose but otherwise will work even if the input to be taped is set to DVI. My confusion was that I had an S-Video input and Composite to the VCR. I now use an S-Video (and a external transformer to get composite) to feed the VCR and now that works. This is solved.

2) I want to be able to watch inputs (DVD for example) on my TV in S-Video or on my projector in DVI. I understand that there is no transposing but just want the S-video output to connect to the S-Video input even when DVI is selected. I can get this to happen with a complex set of configurations described above so I know the hardware can do it, but I shouldn't have to reconfigure the unit in everyday use. This should be a simple software fix. The 990 turns off the S-Video outputs when DVI is selected. This is not solved.