Stuffit is working...
The files are there, but the Finder doesn't want to see them for some reason. I had the same problem. The Finder is just like any other program running on top of the Unix core, in that it will ocasionally have a bug. I noticed that when I dragged the folder into a progam like Toast to back up the folder, the files showed up. I then opened the Terminal and, using a little Unix magic, saw that the were in fact there. What I did was open the folder and then relaunched the Finder with a 3rd party program called Xupport. If you don't have that, simple hit Option-Command-Esc (all 3 at once) and relaunch the finder. I'm not sure if you need to be in the problem folder when you do so, but that's what I did, and it worked.
Hope that helps