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Similar Problem Here
I tried to run version 2.5 with Smart Update this morning and it finally brought the machine to standstill with several minutes elapsing before mouse clicks were acknowledged. iTunes stopped playing (would actually give a few seconds of music every few minutes) and command-tab to move between windows was ignored ass well. According to Activity Monitor "windowserv_" was the biggest CPU user but it rarely spiked above 70%. After an hour of this and no progress on the copy stats (was stuck at 24.72 GB copied) in SD I stopped the copy and everything came back to life.
15" 2.4GHz MBP
4GB Ram
OSX 10.5.1
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