I was having troubles with Stuffit Expander -- when expanding a known non-empty archive, I would get empty archives when expanding. I have found that, in Stuffi's Preferences, a possible workaround. Open the Preferences, click on Destination, and in the Create Surrounding Folder section, click Always. After I changed this setting, expanding an archive no longer resulted in an empty folder.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20050724091440689