This appears to be pop only, but someone might want to verify this on IMAP also. Currently any folder that has subfolders also gets all of the special folders (Inbox, trash, unsent messages, etc). My guess is that this is because special folder creation code depends on depth == 0 and I don't think depth is being set for local folders.
This must be the problem. Imap does set up depth correctly. I thought pop3 does that too. Scott, you can reassign the bug to me if you want. But, you are certainly welcome to own it. :)
I have a fix for this. marking M9.
To verify this you will have to first delete all of the unwanted special folders from your harddrive and then run this. Now new special folders shouldn't be created (unless they are in the top level).
Win_nt 4.0 (1999-08-20-16 M9) I verified that a subfolder no longer gets all of the special folders. And When I deleted all of the unwanted special folders from my harddrive and then run this, I do not get special folders in both POP and IMAP.