I think I have found a work around. So far I have tried: another 990 (Thanks Outlaws), firmware updates, configuration changes, etc. I finally discovered that the Thumping was coming from the subs only and if I did not use the balanced LFE output from the 990, everything else worked very well. I now have an unbalanced connection from the 990 to the SMS1 and a balanced connection from the SMS1 to the Sampson SX 2800. I am also using balanced connections from the 990 to the ATI 3005's "Pure Balance" inputs. It is now very quiet with no Thumping during muting or switching between DSP modes or inputs. I tried a number of different cabling configurations and using the unbalanced LFE output of the 990 was the ticket.