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Probably the other processes on your machine get CPU starved while the application is running flat out. The screen saver runs at a lower priority (hence it is always a few fps slower) so it doesn't stall because other processes get a greater amount of time. Do you have AppleShare running or anything else that would be a background task but have time sensitive requirements? Since you see this in the application you could probably get a lot of information from "top" in the terminal.
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