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I came across this bug a while ago, when I compared the two resent Compare It shell extension packages (the latest wincmpext.zip and the previous one with wincmpext.dll file names).
When I compare the wincmpext.zip files with Synchronize It, the file in 'x64' directory is always missing from the target side. If I extract the files and then compare the directorys it works.
Here's the files in case you need them: http://rapidshare.com/files/282245125/test.zip.html