A little late for the original poster, but nonetheless...

I was having the same problem with my new 990, configured for 4.0, generating way too much bass when listening to stereo sources and after more research I think I understand what's going on now. The short answer, perhaps counterintuitive, is that you can fix your problem if you go into the Speaker Size configuration and set your subwoofer size to "LFE only".

Here's what I think's happening. If you think about what PL II or DTS does when it's creating surround from stereo, it's generating the center, surround and subwoofer tracks from a two channel source, essentially out of thin air. After doing this, the 990 routes the (newly created) .1 LFE track to the subwoofer, but if you've set your subwoofer size to "NONE" then that LFE track gets mixed back into your "large" speakers, effectively adding in extra very low bass.

But if you instead set your subwoofer size to "LFE only", the 990 sends the .1 LFE track to the subwoofer jack instead of mixing it into your "large" speakers. This track is then lost (since you don't actually have a subwoofer attached), but that's what you want. CDs sound fantastic in surround here with this setting.

Remember to set the size back to "NONE" whenever you're listening to true 5.1 (or better) source material (e.g. SACD, DVD-A, or 5.1 movies) or else you'll be missing bass in those cases.

It's a pity the 990 can't do this automagically, but perhaps the real fault lies in the definition of the music surround modes for PL II and DTS because that's just way too much bass for most stereo sources.