Have you tried remapping the CRM user .
1. Launch CRM as an Administrator
2. Open the Users Settings
3. Open effected User Account
4. Change the Domain Logon Name to be a different user account that does not exist as a user in CRM (You could create a new dummy user account in AD).
5. Select Save and Close
6. Open effected User Account again, and change the Domain Logon Name back to the effected user account
7. Select Save and Close
8. Test accessing CRM with effected user’s account after closing and reopening the IE windows or probably after doing an IE reset
Note: Please make sure you have the fresh backup of the CRM databases before following the above steps in your CRM Server.
Thanks,
Mohammad