OK i think the resolution of your monitor has something to do with it, are you playing your games at 1920 x 1080? i'm aware that the 7900GS is a good card but it can't handle that resolution so easily on games..
The bigger the resolution, the harder you push the Video Card.
And the other thing, why would you keep Skype open when gaming? I think that's the other consideration.
Check your statements:
Effects ON, Gaming, ALT+TAB (for Skype) = Situation Nº1
Effects OFF, Skype open, Gaming = Situation Nº2
The common factor here is Skype, why don't you try these?
1) Effects ON, Gaming, Skype closed completely, no ALT+TAB
2) Effects OFF, Gaming, Skype closed completely, no ALT+TAB
See the results... IF the game is not dropping FPS all of a sudden, or even if the game starts without any FPS drop, then you have your primary suspect; Skype!
My .02 cents