I'm running X3 and even it still has some Vista issues but runs with only minor
problems using "run as administrator" as Steve suggests.
I have had the same problem with opening some ufo files and finally caught on to the fact they seemed to be connected to whether or not I physically typed in the ".ufo" file extension. I have not had a problem since.
The bad files are hopelessly corrupted and still reside in my folder, I can not figure out how to get rid of them.