After trying to set up Mail.app to remotely access my unix workplace email, I experienced two symptoms: (1) My entire home directory tree at my workplace was being read by Mail.app which was interpreting every file from .cshrc on up as a mailbox (a bit scary -- is it editing those files to mark them "read"?). (2) Mail.app would just hang, so I would have to force-quit it, and if I restarted it it would start out in a hung state, so it was totally useless.
Read the rest of the article for the troubleshooting steps and solution...
I had been having trouble getting any set of account settings in Mail.app to work, thanks to the lack of any kind of help (the lifesaver bouncing many times before allowing me to search from scratch for the help I need might be tolerable if the resulting "help" turned out to be something better than "enter the settings for your account". That's no help!)
Not seeing any solution, I spent a lot of time looking into all the third party mail readers out there, since although ssh and pine work fine, I happen to want something GUIer (maybe here on a Mac site I won't get puzzled stares when I say this, like happens at my workplace.) I slowly learned the hard way that none of them can handle secure IMAP or POP except Netscape mail, which is mindbogglingly slow in responding to even the simplest clicks, so I had to return to trying to fix the Mail.app problem.
After poring over many archives to no avail, I finally saw a MacOSXHints tip which led me in the right direction: Throw ~/Library/Mail in the Trash (I hadn't yet built up any mailboxes I cared about.) Then I could restart Mail.app, and it was responsive for long enough that I could use its preferences to disable all the accounts I had tried making (I wasn't sure at first which one had started "working" in this way) and not include them when checking for new mail (it was still trying to interpret my entire remote home directory through IMAP as I did this.)
I probably could have thrown ~/Library/Preferences/com.apple.mail.plist in the trash too, and started over from scratch, or I could have double clicked it to edit it with the Property List Editor.
I could then quit, trash ~Library/Mail and restart Mail.app yet again, and now it finally peacefully did nothing but respond to my clicks.
I discovered that the "hung" state is merely a (very severe) performance decline when there are a lot of mailboxes (like hundreds), which we now see can easily happen if things are configured wrong.
So how do we now fix the configuration? For IMAP, the "Account Path Prefix" had been blank (which I guess was defaulting to my home directory on the remote system), so I tried changing it to /var/spool/mail/cook (which of course is not a path prefix of any account, it's just the filename of my remote mail file) and now I can finally finally read my mail with Mail.app!
Mac OS X Hints