If it's a bug, then surely it must be reproducible in a new .capx. If you can't reproduce, then there is little Ashley can do, especially if it's a very large game.
It would also help to say what version of C2 you are currently using.
Have you tried an earlier backup?
The general method for bug finding is to load an earlier version, and check carefully as you re-add the newer features, and hopefully determine what is breaking your game.