iBooks is stubborn about caching book covers. If it sees something different in the epub, it will assume that it's a newer version of the book.
If you're comfortable using the Tweak Book feature, you can open the OPF file and change the timestamp. That should be enough to force iBooks to recognize the change.
After exploding the file, look for the calibre timestamp in the <metadata> section:
Quote:
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<meta name="calibre:timestamp" content="2012-07-07T10:11:42.438277+00:00"/>
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Change any part of the timestamp, rebuild, and that should do it.
G