I repositioned my speakers and wanted to run the auto-set up again.

It didnt register wek=ll, so it told me to change the speaker settings and power down and rerun the auto set up again. So I changed the speaker size and Xover settings and turned off the 990.

Now I cannot get the remote to work the 990! It lights up fine, the batteries are very new still, and no matter what button I push, I get no response from the 990 itself. What do I need to push or do to get the 990 to recognize the remote?

Just to check - you have pressed the "TNR" button on the top, right?

Uhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...

I will double check

PS I am having an EXTEREMELY tough time getting the auto set up to work. It keeps saying that because the front speakers are small and the rears are large to chhange them after turning the unit off.

I am, and my fronts are huge (Klipsch RF7 with dual 10 inch woofers. I have the frequencies set set 40 for the mains, 80 for the center and 80 for the surrounds. I have the 3 fronts set to large and the surrounds to small, and the sub at L & R and LFE.

Two things to try: make sure the microphone is up at ear level (a camera tripod or even a spare box can help with this), and try setting the front crossover to 80Hz temporarily while running the auto-setup.

The "TNR" button worked.

I will try the 80 hz, but I think I had tried that on all 5 speakers.

Nope, still getting the same message...

Im still trouble shooting, but for some reason I am hearing audio on my TV when I run a hdmi/dvi cable to the 990, and a dvi/hdmi cable to the TV. Weird......

This has been reported by several other people. The 990's DVI switching is "dual link" DVI, whereas HDMI's video section is basically "single link" DVI with a different plug. As a result, if you have dual-link DVI connectors on your DVI-to-HDMI cables, the HDMI audio signal can pass through the DVI connector, through the 990's switching, through the second DVI connector, and out the HDMI at the other end.