There are times that I've noticed that, even if nothing has changed in a project, the MDS file gets updated between running the automation or between two different machines.
So, it MAY be possible that, while TECHNICALLY the MDS file has not changed, there are those minor differences between machines, project runs, etc, that would update a project causing the version on your hard-drive to be out of sync with your version in TFS.
One way that the MDS file changes between runs has to do with the use of Project variables. If you're creating and destroying temporary variables during the course of a test run or updating values in variables during that test run, it is possible that the MDS file will be different, prompting the "check out" message.
