The same exact thing just happened me yesterday when I installed KJFK and PHNL on FSX! You say it works fine now, so I will run FSX later today to check it out and see if it is one of those you need to refresh the computer by shutting down and restarting the sim! Maybe it is a memory cache glitch and the memory needs to refresh so that it reads the scenery is suppose to be active!
I am in the middle of Splinter Cell Conviction (Aweessoome game), so I will have to check that out later today! At least you got a response!