For some reason lately I have been periodically getting "... you are not authorized to access [filename.extension] ..." after clicking on the Check-In button in the "Pending Changes" section of the "Team Explorer" tab in Visual Studio.
I can't explain why this happens, but the workaround I've discovered is to click the "Refresh" button at the top of the dialog. Once the refresh is complete, the check-in process seems to work fine. I hope it works for you as well.
If you have run into the same and can explain why, please share in the comments.
Happy coding!