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It's usually not the overt programs which cause stuttering, it's the covert ones. Those sneaky little clock-cycle-stealers which are running in the background. My main development system is prone to that, too. The Aquarium will start hesitating, and I'll bring up the Task Manager. Nothing obvious running, besides occasional flickers in processes, but the changes only last an instant and are gone before I can even see which process it was. Then after a few minutes, the Aquarium will smooth out, and I'll sometimes get a message like, "Your Norton Antivirus has just been updated".
I'm not sure if it will do any good, but you can bump the Priority of the Aquarium up one notch by pressing the Q key. You can also adjust the program's internal Sleep() time, which determines how many clock cycles to give away, by using the UP and DOWN ARROW keys.
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