The folders that re-creating themselves:
I have filters set so these messages should be going into the appropriate folders. Everything was working just fine on my old iBook G4. Mail on my iBook G4 (running OS X Tiger 10.4.11) still works just fine. When I got my new MacPro, strange problems started with Apple Mail ....
I'm using Snow Leopard 10.6.2.
The duplicate messages are going into dozens, most likely hundreds, of other folders. I disabled all three of my Clearwire e-mail accounts, but the duplicate messages still keep on coming ....
My DreamHost accounts are set up in Apple Mail, using POP.
I'm really not sure what you are talking about when you mention the advanced mail account features ....
I still have mail that arrives in the Inbox. All of my important e-mail is filtered to the appropriate folders. The filters are working just fine.
Problem is these self-creating folders, and some mail (not much though) is coming into these mystery folders, even though I have the filters set correctly.