I *think* it has more to do with frame rate than the actual minimizing of the window. This happens to me when swimming, or levitating for that matter, whenever the frame rate drops - and it just so happens EQ takes a rather large frame rate hit whenever it isn't the selected window, or at least for me.
There's a lot of stuff that was tied into the frame rate. Mouse look and spell gem icon refresh (I know the spell icon refresh thing was eventually changed, but no idea when or if it is here) are two that immediately pop into mind.
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