I also had a porked install, with ghost Aeyes pits in the new campaigns.
But I was able to easily fix the problem. I had F4AF installed in the default "C:\Program Files(x86)\Lead Pursuit\" directory in Windows 7 64 bit, so I uninstalled F4AF and re-installed in "C:\Lead Pursuit\Battlefield Operations". I then patched to 1.0.13, installed HiTiles, installed all three Aeyes pits, started F4AF and setup graphics, controllers, etc, and closed F4AF. I then installed the Skunkworks v2 mod, restarted F4AF, and everything worked perfectly.
Hope this helps...your mileage may vary.
There are no accidents and no fatal flaws in the machines; there are only pilots with the wrong stuff.
Tom Wolfe, The Right Stuff,1979.