Newer versions of Dovecot contain updates to the handling of uidlist files - the issues of which, may lead to difficulties when receiving emails via POP3 or IMAP. It may be a good idea to update your installation.
Atmail 6.3.6 uses the 1.2 branch; newer versions of this branch are available for download via: http://www.dovecot.org/download.html
To update, just do the following:
1.) Download the latest sources from the above link:
% wget "http://www.dovecot.org/releases/1.2/dovecot-1.2.17.tar.gz"
2.) Untar, then go into the untarred directory:
% tar xvfz dovecot-1.2.17.tar.gz
% cd dovecot-1.2.17
3.) Stop the Atmail service:
% /etc/init.d/atmailserver stop
4.) Configure, install:
% ./configure --prefix=/usr/local/atmail/mailserver/ --with-mysql --with-ldap --with-docs=no
% make && make install
5.) Start the Atmail service:
% /etc/init.d/atmailserver restart
Congratulations! Now you have the latest Dovecot binaries installed.