This problem was found running ITMS Build 0104 running Suse 7.2:
Support Request ID: 521504
Executive Summary: Users can't login due to web server's implementation on crypt function

Fix Details:
In toolbox.php, in the function db_add_user, replace line 
872 with:
$query = "INSERT INTO ldap (name, password) VALUES ('$newusername', '" . crypt($newpassword, substr($newpassword, 0, 2)) . "')";

Also in toolbox.php in the function ldap_add_user, replace line
855 with:
$info["password"] =  crypt($newpassword, substr($newpassword, 0, 2))


Note:
Provided in this patch are versions of toolbox.php for ITMS Oracle Patch (build 0104) and ITMS (build 0104) with the above changes applied