This is really irritating. I am currently in a loop between two mailboxes. Change to one. Status bar says there is new mail in a folder. Change to it. No new mail. Status bar says there is new mail in a folder. Change to that. No new mail. And again and again. So mutt might not actually say there is new mail in the mailbox, but it just says Inc:1 in the status bar. So it's not losing whatever marker it has for unread mail in a mailbox. Could this help with troubleshooting?
-Ken