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I am not sure yet if I can reproduce the problem reliably, but it is seems that this time-out happens when I run SD! shortly after I did a fresh login.
That would also explain why I had the problem often after upgrading to Leopard and now only sporadically. The first weeks after upgrading I did a fair lot of adding, replacing or deleting software, reorganizing things on my Mac, often followed by a restart or log-out and again log-in. I did that usually at the end of the day, before I finally let SD! do the backup and shutdown.
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