Well, I very well might have stumbled upon something. Possibly a bug/issue (whatever you want to call it) in the 990.
I thought for the heck of it I would unplug the left/right analog connection from my digital set top box to my 990, leaving only the coax cable hooked up. Well, it has been 2 days so far, and not once has it errantly defaulted to Pro Logic II Movie. Every single Dolby Digital broadcast has correctly set the 990 to Dolby Digital. I'm gonna give it a week before I completely make up my mind that I found the issue.
Unfortunately this sucks (if this is in fact the issue), because my zone two setup can't receive audio unless the analog connections are connected. If this proves to be the issue, it almost seems like the 990 isn't properly automatically making use of the supplied digital signal.