It could be that the bundle bit got reset on the affected folders. If you have Developer Tools installed you can use GetFileInfo command in Terminal to find out. Here's an example:
NoobiX:~ francine$ GetFileInfo /Users/francine/Desktop/screens/
directory: "/Users/francine/Desktop/screens/"
attributes: avBstClinmed
created: 02/17/2007 11:18:19
modified: 06/20/2007 14:10:06
The capital "B" in the attributes means the bundle bit is set so the Finder treats the folder as a package. To change it back you use the SetFile command (also installed with Developer Tools):
NoobiX:~ francine$ SetFile -a b /Users/francine/Desktop/screens/
For additional information see an article I wrote on the related invisible bit being set problem:
http://www.pinkmutant.com/articles/invisible.html
There's a link to download the two commands you need so you can use them without installing all of Developer tools.
Francine
Francine
Schwieder