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I'm having the same problem. [ATTACH]
This would make automatic daily backups possible through Super Duper, too, which is what I desperately need.
Windows close at regular speed if I exit Tools. But upon restarting my mouse ceases to work, so the solution is imperfect.
Same problem here with build 3214 on a MBP 2.2 Core 2 Duo with 4 gigs. Ugghhhh... I guess I'll try disabling Tools for now; what can we expect...