I've got a linux server with a kludged UW imapd that supports maildir folders.
zimbra desktop didn't allow/ask me for a prefix for my mail folders, it started inventorying my entire home directory (bad).
When it got to one of the maildir files, it crashed (worse) (foo.example.com below was the real name of my server):
com.zimbra.cs.mailbox.MailServiceException: invalid name: 1208566437.13841_1.foo.example.com,U=5
Code:mail.INVALID_NAME Argname, STR, "1208566437.13841_1.foo.example.com,U=543118,W=131 039:2,S
at com.zimbra.cs.mailbox.MailServiceException.INVALID _NAME(MailServiceException.java:312)
I'm running zimbra desktop on OSX 10.5.current, downloaded today (10 june 2008).
hope this report helps.