After upgrading to Dovecot-1.2.2 from 1.1* subfolders disappeared, though it was possible to access them directly, e.g. with "mutt -f =lists/dovecot". The problem only occurs if the listescape plugin is enabled. Some relevant bits from the configuration:

namespace private { # The only namespace. separator = / prefix = inbox = yes } protocol imap { mail_plugins = fts fts_squat listescape }