Have you got host intrusion prevention agent installed on that system?
As per application control best practice document, if you have HIPS installed on a system, it is safe to disable memory protection in App Ctrl.
HIPS is not installed on the machine
Please check if the Policy got applied on the endpoint. Also the policy will be applicable for the next run of the application(which I dont think is the issue here).
If you still dont see success, please file a case with support.