Yeah, I have had the same issue, even with the old firmware. Two things were involved in my situation.

1. My DVR box had hand-shake issues with the 990. For some reason, it just wouldn't always lock the Dolby Digital signal, even when truly a Dolby Digital signal was being sent. I would then subsequently select "Dolby Modes" and the 990 would then allow me to choose "Dolby Digital". Due to other reasons, the cable company switched out my DVR box to a completely different model and the 990 no longer exhibits this behavior.

2. On page 25 of the 990's manual, there is the following listed...
NOTE: The Model 990 defaults to Dolby Pro Logic II(x) Movie mode with any source device supplying Dolby Digital 2.0 or PCM sources
This is an annoyance to me because no matter what setting I have selected for a program (like Dolby VS 5-SP WIDE), if the program that I am watching goes to commercial which is Dolby Digital 2.0, it switches to Prolic II Movie. Then when the show returns to what I was watching, I have to flip it back to "Dolby VS 5-SP WIDE" manually. That gets annoying every commercial.

My issues may be similar to yours, or might not be related at all. I just thought I'd mention them.

I guess I have learned to deal with it.