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I actually have had just that same issue - the app itself doesn't seem to be pinwheeling - menus are responsive, as is the rest of my system.
However, the copying process itself seems to be stuck - for about ~45 mins., the progress bar hasn't moved, and there's nothing to suggest that there are any files being copied (there's no change in the number of files copied, or evaluated).
This is on a Smart Update, on a cloned backup which hadn't been updated in some time (about two-three months) - is it just because SD! is taking an extra long time to examine all of those older files for updating?
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