Switching from a procmail + maildir setup to using dovecot, you may run into an issue where dovecot does not recognize your maildir subdirectories (subfolders). The suggested fix using "LAYOUT=fs" does not work at all and when you enable debugging (mail_debug = yes), you see the following in syslog, which means you have no inbox and no mail.
[info] dovecot: IMAP(your_user_name): maildir: data=~/.maildir:LAYOUT=fs [info] dovecot: IMAP(your_user_name): fs: root=/home/your_user_name/.maildir, index=, control=, inbox=
I got around this by symlinking ~/.maildir/INBOX to ~/.maildir/. Apparently, dovecot really wants to see an "INBOX". My relevant mutt settings follow:
set spoolfile=imaps://username@hostname/ set folder=imaps://username@hostname/