Windchill Users can checkout, but not check in

Wow, this like the anti-roach motel. Can you send the methodserver log for that access error?

Sounds like it might be an ACL problem. I believe the scenario you described would occur for CAD or WTDocuments (objects with files) if the Modify permission was granted but the Modify Content permission was missing. You can access the ACLs at the Site/Org/Product>Utilities>Policy Administration and here's the Access Permissions Help Documentation that describe the various permissions.

Here's a screenshot of our ACLs changed to use the more out of the box In Work and Released states.

Side note: The Set State permission on the Released row allows using Promotion Requests to get objects to Released (this is not obvious in the Help Documentation). Modify would allow using Promotions Requests but gives the undesired ability to checkout Released objects. We've disabled Set State transitions in the Lifecycle to prevent users from using the Set State command.

Double check that you don't have any "deny" ACLs assigned that might block access. If you have a deny set against Team Members, or perhaps All States, it might trump the access that you're trying to provision.