This has happened three times with different accounts so it may not be a fluke. Sometimes the folders I have created in web interface are not there. If i use the edit/new folder and create a folder with the same name it appears and all the mail I had copied into it is still there. The first time it happened I freaked because i thought I had lost a bunch of mail. I am waiting for it to happen again so I can look at the server folders before recreating the folder in the web interface. The default folders do not seem to be affected just ones I created with the web interface. I have not tried to logout and back to see if they reappear.
Thanks