Have used quite a few MSC-400 and found none of your issues. I have a SageTV setup and find zero lag on transport controls. Are you sending the IR from the remote to the MSC-400 or doing it the proper way and just sending a Trigger? Your SageTV device should be in the MSC and NOT the 980. Then you drag the triggers form the MSC to the buttons on the 980. I never put any IR codes onto the remote unless they're absolutely needed.

The position of the 980 should have zero effect on reception. I have a customers 4 story 7000 sq ft house using 1 antenna on 3 floors with zero issues. The only codes in any remote are for the TV and everything else is a trigger.

I wonder if the residual RF you speak of is interference? A 15 x 13 room is small, at my house I had 1 antenna for the entire house with no issues.