using the roundcube that comes with Kolab 3.1 Alpha (roundcubemail-1.0-0.7.dev20130809.git328876.el6.kolab_3.1.noarch)
I can set the label, but it does not appear in the messages list. Therefore it is not possible to remove the label by clicking on it.
The only way of fixing it was to add a line in method fetch_headers($folder, $msgs, $sort = true, $force = false) near https://github.com/roundcube/roundcubemail/blob/master/program/lib/Roundcube/rcube_imap.php#L1074
and setting $force = true;
There should be a better way though, but I am still learning about Roundcube plugins...