This is more than likely a GPO issue, Somewhere there will be a write or read restriction imposed on the group of users that are failing. try comparing the applied group policy from a user that works and one that doesn't.
The only times I have ever had upgrade issues with Pulse it has come down to GPO getting in the way.
Try running WinAudit, and compare the outputs, JTEC will generally ask for the output from this when you have permissions issues.
Senior Security Engineer
JNCIS-SA, JNCIA-FWV, JNCIA-JUNOS
CCSA, CCSE CCEPE, CCNA, ACWA F5-CA