In case this happens to anyone in the future, I am posting the response I got from Outlaw support:

You are either experiencing some sort of RF interference or the processor may have corrupt data that is affecting it's switching logic. In theory this should not be able to occur but if the processor has corrupt values it may not carry out switching as it should.

If the tape input is reversed with the output you could have weird problems, if something was accidentally plugged in when the unit was live it could cause a problem with switching. Because I've never encountered this problem with the 990 platform my guess is that resetting the processor to it's factory defaults as outlined on page 48 of the manual will restore normal operation. You'll have to reconfigure each source label for the correct input type. I'd also recommend using a digital connection from the X Box as it is capable of delivering 5.1 Dolby digital to the processor. If the reset does not fix the problem I would recommend disconnecting each source one by one to see if it ceases to exist. RF noise if close to an input can bleed through to other inputs. Also check your connections, if any cables have an arrow( --> ) to indicate signal flow be sure they are in the direction of the signal, from CD to pre or pre to amp. A directional cable that is installed backwards can act as an antenna of sorts and pick up stray RF, this could explain the muted sound appearing across inputs. Please re-open this ticket if you need assistance.

Thanks for sharing that with us, kgt - it's good stuff, and it sounds like you're on track to getting a solution to your problem.