As this comment from TeddyTheBear shows, there is a problem with Stuffit Expander expanding an archive but producing invisible files. The problem can manifest itself in very scary ways, giving the impression that data was lost. Sometimes an archive will expand into an empty folder, or sometimes the folder will contain only one or two files (when it should contain many more), or sometimes only one or two files would be "missing" (invisible). In actuality if the archive expanded without errors all of the data probably came out okay. if you use Terminal to look at the expanded folder you should see all the "missing" files and folders. They are just not visible in the Finder.
This typically happens if you have Finder -> View -> ShowViewOptions -> ShowItemInfo enabled.
Jamie Zawinski points out that the best solution for the problem is to just create a new folder in the folder that contains the "missing" data. This is enough to make the Finder suddenly show all the previously invisible files.
It would be nice if the owners of Stuffit would fix this bug. But don't hold your breath.
Mac OS X Hints
http://hints.macworld.com/article.php?story=2006072300495478