This is an issue reported by a iRedMail user moment ago, and i'd like to share the solution here:

Problem

Users can't login via POP3/IMAP after importing user accounts from 0.4.0 to 0.5.1.

Root case

As mentioned in Upgrade Tutorial (0.5.0 -> 0.5.1), there's an small improvement of POP3S/IMAPS service restriction in section 'Enable POP3S/IMAPS services for all mail users'.

Migrate or upgrade from v0.5.0 or even older versions should also apply this update, so that LDAP query can get correct result.

Solution

Just apply the update in section 'Enable POP3S/IMAPS services for all mail users'.