I had that prefix window come up for my fastmail.fm account and until a few days ago resisted letting Mail.app add the prefix. Even though the account is supposed to use the prefix, it had worked for years without it, so why change it.

But I did. And after some hours of trying, the mailboxes not showing up, or the sent, trash, etc. folders on the server not being recognized at such, deleting the account and starting from scratch and copying everything from the server worked. And for better or for worse, the imap folders are grouped along with the rest, away from the inbox. Certainly a bit frustrating that Apple didn't deal with this a little more smoothly.

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