I've noticed that the software upgrade doesn't address the bass management A/D/A issue when using the 7.1 Direct, which I was hoping would be resolved. I've been thinking of buying the SMS-1 anyway, but will using the SMS-1 allow me to avoid having the analog multichannel output signal from my universal player (Pioneer Elite DV-79AVI) go through any processing within the 990 without having to adjust speaker size, etc.?
If so, would someone explain to me how to accomplish this with the SMS-1?

If you're considering an SMS-1, definitely check out Outlaw's new guide .

The SMS-1 is at best a two-channel device (and in most applications it is purely a subwoofer device) - I can't think of a single way to use it to avoid the A/D/A process on the 990's 7.1 Direct inputs. Sorry...

I was apprehensive about the 990's A/D/A as well, having sold off my ICBM, but cannot say that I miss it. It does a good job without any degradation in the signal that I can hear. It actually comes in handy when using the Toshiba HDDVD player.

Thanks. I suspected that the SMS-1 wouldn't do a thing for avoiding the extra A/D/A conversion, but I thought that I'd ask anyway.
I wasn't going to download the update since it doesn't do what I was looking for, but I'm glad that I did it anyway. The change in SQ for the PLII and PLIIx modes was a nice surprise. I thought I was imagining the improvement until you folks on this forum confirmed it.
Another thing that I noticed was that I had to turn down the gain on my sub amp quite a bit after the update. Did anyone else experience this, or am I finally going off the deep end?

I also had to turn down the gain on the sub from 5+ to 0 after the update.

Same here. I definitely had to turn down my sub's gain after the firmware upgrade.

Glad I'm not alone on the sub gain. This is probably why the sub trim bug was quickly encountered by several people.