I had the same problem too.
When I had EQ up in full screen, I would pop out to desktop and the game would be in windowed mode if I clicked on any object on my desktop through the EQ UI. This included clicking in the EQ UI's chat box (which I had positioned at the bottom of the screen) because in actuality, I was clicking on the Windows Vista task bar. I also had trouble looting things from corpses, as I would be clicking on desktop icons arranged on the left side of my screen.
You'll also notice that the EQ cursor will change to your standard white Windows cursor when you're about to click something on your desktop, even though you're looking at EQ in full screen.
I hope this helps shed some light on the topic.
Much love.
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