i can notice a severe performance drop when playing war commander (a basic flash facebook game) in normal window inside the browser, however, if i put the game in fullscreen, it works perfectly.
i use firefox and have a gtx260.
Remember when the game is full screen, your GFX card is only processing the game, but when you are in window mode it has to process the game and the desktop. At least that is how I understand it. I could be wrong...
It should be able to you are correct. I take it this is a recent problem. If so, I would check to see if anything has changed recently, perhaps the GPU is no longer being cooled properly so I would check internal temperatures. See if anything has been installed without you knowing it that may be running consuming more resources than it should.