I had the same problem (email sent from my roundcube webmail to hotmail went in the thrash). I changed the line
$rcmail_config['useragent'] = 'RoundCube Webmail';
in config/main.inc.php to
$rcmail_config['useragent'] = 'SquirrelMail/1.5.1';
...and the problem was gone. If You can live with the fact that the header lies to you, and says that the email is being sent from squirrelmail instead, then this ugly little trick might cover up the problem, at least for the time being.