Windows 7: The color scheme has been changed/Windows has detected that your...

For as long as I can remember I have had these warnings/errors on my computer:
"The color scheme has been changed to windows 7 basic"
"Windows has detected that your computer's performance is slow"
The first one automatically changes the color scheme to basic. This would not be a problem but when it does this my onscreen graphics go very choppy.
Over the months I have found that this seems to only happen when:
I have 3 monitors connected (one running from each graphics card)
Autocad and inventor are open one 2 screens.
Also I have noticed that it does it less when I have the third monitor blank with no windows open. It does it less when I run 2 monitors from 1 card and 1 monitor from another card. Frame rate and responsiveness are at worst with 3 monitors in 3 cards, slightly better with 2 screens in 1 card and 1 in another card and a lot better with just 2 screens in one card and the 3rd screen disconnected.
I have searched on here and on google and found lots of people with the same issue, some relating to program compatibility and some to graphics cards etc.

Some of the things I have tried:
Turning off compatibility mode
Updating graphics cards drivers
Using the aero troubleshooter
Using a crossfire cable and running 2 monitors in 1 card and 1 in another
Adjusted various performance options in system properties.
A number of other things that don't just come to mind.



Can anyone help me to either stop the aero theme being changed or make it so the basic theme doesn't mess with my onscreen graphics?

PC details:
Windows 7 pro 64bit
intel core i7-2600k @3.4GHz
16GB RAM
3 x AMD Radeon 6700 HD Graphics cards
3 x Prolite 24" monitors