I have something similar to this happen. It's like when the window looses focus it tries to run in "Less-system-hog" mode, but when the window's still up, it causes the whole screen to do it. From what I remember, I just make sure to actually minimize EQ2 first if I'm working in other applications.
Sometimes I get this when photoshop and eq2 are both open, and some other's. And sometimes it can happen by itself if I recall.
Just try minimizing applications when they're onscreen and not in use.
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