I actually did do that shortly after I got the 990 just to make sure I had the latest firmware. It is an issue with the bass management for sure.

The 2 fixes that I can think of are to either have the 2 channel sub offset go in both directions, up & down or have each input have its own bass management settings applied.

I love this pre/pro but this particular issue is frustrating and made me wish I had looked at some other options. I also paid $999 2 months ago and now they are $799, that also stings a bit too