I've recently been dealing with unpleasant boomy bass when the 990 automatically switches to Dolby Pro Logic:Movie mode as the content from my cable box changes.

I've discovered that if you don't disable crossover at the sub, and leave the sub crossover set near to the 990 xover setting for the fronts, the automatic switch to Prologic II:Movie is nowhere near as unpleasant.

What are your mains set to, large or small?

The mains are set to small, xover at 60. I also noticed that the surrounds were crossed over at 100 and I dropped them down to 60. That seemed to help a bit more.

So your having to turn on the active crossover at the sub (60hz) to fix the problem?

I wouldn't call it so much a fix but an improvement. To keep this in perspective, I never actually leave the 990 set at ProLogic II movie, so it's not a crisis, just an annoyance until I select a more appropriate mode.

Now to complicate matters, I just picked up a Cambridge Audio 840C. It's not broken in yet, but I can already tell that I'm going to want to leave that sub crossover switched out going forward. I'll try feeding the cable box digital out through the 840C to see if it can clean things up.