After some tests I've found a reason for auto archive on send issue.
But I've got nice message in error log
[28-May-2013 10:07:30] PHP Warning: array_shift() expects parameter 1 to be array, object given in /var/www/<...>/modules/CRM/Roundcube/RC/plugins/epesi_archive/epesi_archive.php on line 331
I've fixed this, and now it works, but still I can't find a reason for normal archive action. It works for me as it should. Both - sent and received messages are archived properly.
Log messages depends on logging level of php set in modules/CRM/Roundcube/RC/program/include/iniset.php
Make sure that it's something like E_ALL &~ (E_NOTICE | E_STRICT)
Another option to find some useful debug logs is to enable RoundCube logging in /modules/CRM/Roundcube/RC/config/main.inc.php
Please be aware that your password may be shown in log messages (e.g. imap log).
I've attached fix for auto archive issue. Please test and report is this working for you.