I think this may have fixed it. So far so good.
This is my set up at work just for reference
Dell Optiplex 980
Core i7 860
8GB Ram
Two Radeon 4550 w/512MB each(was the best Dell offered on that model)
3 LCD monitors with 1 Rotated
Win7 x64
Only seems to happen when using Internet Explorer 9 or Firefox 4 on one of the other monitors.
I have the latest ATI Drivers (Catalyst 11.3) and other driver updates and EFI/BIOS updates.
I have not installed SP1 for Windows 7 X64 but I am not sure that would do anything to solve the issue.
I can run other programs like my XP Virtual Machine and Instant Message windows and even MS Office Applications and it does not cause the issue. I have even played videos using a TV-Tuner and through Media Player without an issue. This problem only seemed
to happen when I upgraded to Firefox 4 and used that and I recently upgraded to IE9 and it happens in there displaying only regular web pages too. It is very frustrating.
If it reoccurs I will be back.
UPDATE: Well I still get the "Windows has detected performance is slow" bubble pop ups but the computer has not disabled aero like it was doing before.
Still does not explain why that is happening at all though. Every one that I have read that has this problem has plenty of Processor/GPU power and Ram to accommodate multiple displays. Seems the only common variable is having dual video cards.