When SD! "repairs permissions", we simply hand off to Disk Utility, which does it for us. If the Mac hung while doing that, there's something wrong with Disk Utility, the drive, or something similar.
Remember, repairing permissions is done on the source, not the destination, so you'll want to check the startup disk. To do so, you'll need to start up from your OSX install DVD...
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--Dave Nanian
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