Chriso2,
The muddy sound is indeed the overlapping bass from the LR + sub reproducing the same signal with phase problems. The bass management is a scrambled egg mess inside the 990. Completely useless.

Regarding the crossover points: I was able to reproduce the reversed crossover (40 is 200) twice while testing with True RTA....and I tried it 5-6 times where I could not reproduce it (i.e 40 was 40). This is very concerning because it implies another as yet undiscovered "factor" that affects the behaviour of the crossover.

AS to running cd into the 7.1, I am not sure. Others here have posted that the 7.1 bass management and the digital bass management works as intended. I am not so sure it does. I also do not know how those inputs will recognize the signal. I am getting more and more convinced that the digital input crossovers are not working as well. My pioneer on digital out to the 990 playing a standard CD gave nearly identical response curves on True RTA as my analog input CD...that is to say it sent a full range to the sub on stereo & upsample.
I don't want to start another hornets nest so I have been refraining from posting that data. I am sure some people will disagree. I don't want a fight I just want it fixed.

Waiting for an update as well,

The Capt