This is still a problem with dovecot 1:2.2.9-1ubuntu2.1. The problem seems that pam searches the modules in /lib/security when invoked from dovecot, but on my system they are in lib/x86_64-linux-gnu/security/ and not found.
Regular login via sshd works, so I think the bug hides in dovecot. I know that I'm reporting about a ubuntu package to the debian maintainers and apologize. But as I found this bug I believe this is the right place to share my findings.