I had the same problem. I'm using X3. I uninstalled Rapture and deleted the patch files, and downloaded fresh patch upgrades from Cakewalk. I reinstalled it in Windows 7 64 bit as an administrator. This worked!
On another note, I rebooted my computer after deleting the old patch files. On reboot, I got a Windows message telling me that my Recycle Bin was corrupt. So, I'm guessing that my old download files might have gotten corrupted.
I had to reload the Expansion Packs. There were some permission problems with them, but after fixing those everything loaded up nicely.