Thanks Jason,
Following your tip I found this wiki explaining how to connect to the SMP 3.0 Derby database.
I downloaded the DbVisualizer client and successfully connected to the database.
It has many tables but it was easy to identify the one called AGENTRY_CLUSTER_USER_AUDIT that contains the field informing if a user/application is already logged on.
I executed the following SQL command to manually log out my user and it worked 
UPDATE AGENTRY_CLUSTER_USER_AUDIT
SET IS_LOGGED_ON = 0
WHERE USER_ID = 'xxxxx'
AND APP_ID = 'SAPWorkMgr6.1_JVA'
