when you edit protocols under "webmin -> servers -> dovecot -> networking and protocols" it actually writes it to the wrong file.
i copied the config folder structure and did a diff to see where it changed, and see that it touched the managesieve config file (that's a dovecot plugin whose protocols line SHOULD be saying "protocols = $protocols sieve" which means that it appends the protocol to the list of existing enabled protocols:
diff -ENwbur /tmp/dove/conf.d/20-managesieve.conf /etc/dovecot/conf.d/20-managesieve.conf --- /tmp/dove/conf.d/20-managesieve.conf 2013-02-16 23:47:04.000000000 -0500 +++ /etc/dovecot/conf.d/20-managesieve.conf 2013-02-16 23:56:27.000000000 -0500 @@ -3,7 +3,7 @@ ## # Uncomment to enable managesieve protocol: -protocols = $protocols sieve +protocols = imap lmtp sieve
so it edited /etc/dovecot/conf.d/20-managesieve.conf, but it SHOULD have edited /etc/dovecot/dovecot.conf, which contains this line:
protocols = imap pop3 lmtp
maybe this is like the postfix example where you use a tool to edit the config and it's out of your hands... i hope not. if you are using a tool then either look into a way to always edit the correct config file, or disable the feature...