possible answer...
My Toshiba HD CRT RPTV (57H83) owners manual cautions that when using a DVI device connected to the TV, watch the order of "turn on".
That is, turn on the TV first, then turn on the DVI source device (or, in you case, the chain of devices that are in the DVI signal path).
When turning off your electronic components, turn off the DVI device(s) first, then the TV.
My understanding is that this is to prevent getting "out of sync" with the DVI signal. So, why is it doing it now, when it didn't do it before? My guess is that now that you have installed the 990, you have changed the order in which you turn on your components.
BTW, before I received my 990, I had been using a Geffen DVI switch box (pretty slick little device actually, with remote control) to switch between the DVI outputs of my Oppo DVD player and my Samsung TS-360 D*TV satellite receiver.
Comparing it's performance with the DVI switching of the 990, I notice no difference in signal quality.
The only other thing that I can think of that could be a factor (although I doubt it, as you say it clears up if you switch to a SD channel, then back to an HD channel) is that now your combined DVI cable length is probably longer then before (when you didn't have DVI switching)...for obvious reasons. You can have signal loss with long DVI cable lengths of poor cable qualtiy. My owner manual cautions against a DVI cable length greater than 3m. However, my combined cable length is on the order of 6 meters, and I have no problem (and other people have DVI lengths of even much greater with no problems). But, you never know. I'd bet my money though that it's the timing issue I mentioned previously.
Just make sure your TV is turned on, ready to receive a DVI signal, before you send it that signal.
Looking at it another way, the TV should be the first on and the last off.
_________________________
990
Adcom 7607
Oppo
Rocket RS 850's, 550's, Polk LS 90's
SVS PB-12 Ultra