I've had a 990 for about a month now. Just upgraded it to the latest firmware the other day. I was happy with the sound of 3.07 but I figured its always a good idea to have the latest firmware (and my sub wasn't working in bypass with 3.07). Now, using the same settings I was happy with before, the sub level in all modes seems much lower, especially in stereo or bypass. I have this sub :
http://www.billfitzmaurice.com/T18.html (I highly recommend building one of these, the driver is only $30 and it sounds real close to Velodyne) It has a plate amp with phase, crossover, and level adjustments. With my older Yamaha receiver, and with version 3.07 of the 990, the amp adjustments that sounded best were about 42hz and "10 o'clock" on the level knob. On the 990 I have Paradigm 9se fronts set to "Large" and 60hz, the rest is set to small and 80hz. I have an OPPO 980 with coax.
My thought is the sub feed seems cleaner (good thing), but doesn't seem to fill in as well on 2 channel (not crossed over correctly?). Its definitely louder now as an LFE. I had it turned up for music then watched a movie and I heard it clip during a gun fight scene. I had never driven that subwoofer to clipping before.
Gonk..I downloaded your DTD disc (which by the way the OPPO 980 won't recognize on CD-R) and I'm going to do some testing today, I just wondered if anyone else experienced the same thing when upgrading firmware. Part of me would like to put it back the way it was.