Originally Posted by OldHarry
There just seems to be something about the way stuff it unzips things that doesn't always unzip everything.
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Well there's your problem...
StuffIt is good for some things. Extracting ZIP files is not always one of them.
Mac OS X's built in ZIP functions work much better.
To give Archive Utility control of .zip files:
Right click on the .zip file, choose "Get Info". In the popup menu in the "Open with:" section of the Get Info window, choose Archive Utility then click "Change All..." then "Continue"
You should find things working out much better.