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Two possibilities -
The most likely culprit is some other program stealing clock cycles. My own machine does this if I'm on-line when the Aquarium is running.
A second possibility is that Vsync is turned off. Video cards are so fast these days that Vsync is almost undetectable, but occasionally you can still see the problem that it was designed to eliminate -- the updating of the screen while the electron gun is still in the middle of painting the previous frame.
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