The different behaviors in your and your wife's experience with Mail's mailboxes may simply be a function of Mail's flakiness in displaying mailboxes which reside on the server. For example, in my .Mac account, my Drafts folder comes and goes. Right now, I don't have one in Mail's sidebar. Several weeks ago, I wanted to save a composed email prior to sending it, and noticed I had no Drafts folder. Saving the message induced the appearance of that folder, but sometime since then, unbeknownst to me until just now, it disappeared again.
A while back, launching Mail always introduced a Junk folder into the sidebar. I would select and delete the smattering of messages contained therein, then successfully delete the mailbox, only to have it reappear on next launch. I assumed that for some reason, the Junk folder on the server was being displayed in Mail's sidebar, but that didn't used to happen, and it's no longer happening.
