Erroneous Older Version Message

I've been working on an older project that was done in Revit 2012.

Sometimes when I go to open the project (using Revit MEP 2012), I get the message to say that the file is from an older version of Revit.
Note: I last saved the file on Wednesday last week and synchronised with Central at the same time. When I came in this morning I got a message to say that the file is from an older version of Revit.

This isn't the first time that it's happened on this project. I've already gone through the upgrade process once, even though it's a 2012 version already.

I don't have any older versions of Revit on my machine. The project was started in the 2012 version.

I've deleted all other files and sub folders from the location for both the central file and the local file and I still get the same message.

There are two linked files in the project. If I open either of these I don't get the message (they are both 2012 versions).

I've sent the file to a colleague and he gets the same message when trying to open the file in Revit MEP 2012.

I also have the 2013 and 2014 versions of Revit on my computer, but these aren't open and haven't been opened since I logged on.

Anybody know what's going on?