Hi Nasir,
Are you by an chance on SP 11? In SP 11 there were few bugs.These bugs were resolved in the note 1824956 & 1817251.
I also assume that you are able to find the user in the tables GRACUSERCONN for the specific connector.
Can you do one thing, Assign a couple of roles (That has violations) to a user, run the Sync job again and then run the risk analysis for that user.
Please make sure that the Value of the configuration parameter 1026 is set as '0'.
Also,if the value of the parameter 1037 is set to "yes",Make sure that you have the supplimentary rules otherwise change this to "NO".
I hope this will help.
Thanks & Regards
Japneet Singh