horrible fps drop after different option in the color scheme error

Hello,

with various games I'd get the error message that "my computer's performance is slow and that i should try to change the color scheme settings to Windows 7 Basic" after a few minutes of playing. (currently with Assassins Creed 3)
I have always clicked on "keep current settings and don't show again" and I'd be rid of the error message without any problems. (until I started the game again at least but that doesn't bother me)
Yesterday however I accidentally clicked on "keep current but ask again if performance stays low".
Since then I'm not getting the error message at all anymore, my fps on the other hand will take a huge nosedive (I'm guessing to below 10) after a few minutes of playing. Alt-tabbing out of the game and going back in does however fix the fps issue, for a few minutes and then it's nosedive again.
World of Warcraft has never given me this error message and is also not experiencing any issues with this.
I don't remember what other games did or did not give me the message so I'm only mentioning those 2 games.
Since the issue started after I clicked a different option in that error message and I'm not getting it anymore I'm assuming it's related to that.
I have tried rebooting, disabling Aero Peek and adjusting the performance of my visual effects to the best performance (control panel -> system -> advanced system settings -> advanced tab -> performance settings) but without any changes.

Any advice would be more than welcome as Assassins Creed 3 (and most likely a bunch of other games) have just become unplayable due to this.

Thanks in advance,
Aki