I ran into a problem with gMail and another POP provider the other day whereby POP mail would download, but fail to show up in Apple Mail. Checked permissions and all was good. In fact, I even went as far as chmoding my home directory recursively to 777 in a bid to troubleshoot the problem. It was to no avail. I then tried recreating the offending account, still to no avail.
After mucking around, Mail gave an error message saying the directory could not be written to (despite all the checks and changes made earlier). There were no readily apparent barriers to creating/modifying files/folders in the Finder (via Get Info) or in the Terminal (via ls -al). It was almost like some other permissions system was in control of the folder.
However, SubEthaEdit was able to show me the directories that were apparently not writable. I recreated all the offending directories by hand, copied in the subdirectories from the original folder, and all was fine again. Strange error.
So in summary:
Symptoms:
Mac OS X Hints
http://hints.macworld.com/article.php?story=20060523052048620