Nope, just because there are DVI pins connected to the cards outputs, they are not connected to any type of DVI circuit in a monitor... therefore they are not seen as a digital display... only pins receiving feed back to the card are the analog pins.
The term DVI to Analog "ADAPTER", versus "CONVERTER", applies here. An adapter just moves wire traces to a different type of connector setup, whereas a converter electrically transforms the signal to something else. Almost all vid-cards at the moment use "dual" DVI-I interfaces... thus carrying both signals, but cannot drive 2 differing standards (with rare exceptions, since VGA is an altered signal from digital).
I agree it has something to do with the CCC drivers and .Net. Even on my 9800 Pro... I get a extremely short "flicker" at launch of log in screen, and at final shutdown. I don't get it while opening CCC in Windows, because I have set .Net's services to automatic. Installation has also incurred a long "black screen" with a very short Windows load screen, versus a long load screen, followed by a short-term black screen to windows log in.