We just upgrade from JIRA 5.0 to JIRA 6.1. We keep the security level (the numeric value) in each user's property and then we use the misc workflow extension to set the "Security Level" equal to the user's property which has that numeric value for the Security level on the Create Issue. Worked perfectly in JIRA 5.0.
Atlassian did a fix on defaulting the security level, not sure it's related. HELP...this is messing up all our users!!