Hi Venu,
Try to run the program RHPROFL0 in Se38 tcode. and Specify the Object type as "S" and Specify postion id which you are facing issue.
Remove the test mode option on the same screen and click on execute.
if it not works then in the same screen specify the object type as "P" and specify the users personnel number and remove the test mode option on the same screen and click on execute.
It will refresh the all role assignment at position level and user level.
I hope it will solve your issue.
Thanks,
Siva