I had to re install FSX and the ngx about a week ago after my hard drive was formatted. After I re-installed the aircraft, I've been having some problems with the FMC.

 

1.) When I try to save a route (this happens before and after executing the route), the Execute button highlights, but when I press it, nothing happens, and I'm forced to press the erase LSK key to continue my flight planning.

 

2.) The options I set don't save. Earlier, for every liver I chose, I could change the options, displays and the pause at top of decent settings to my liking from the FMC, and the next time I loaded the aircraft with the same livery, my changes were saved. Now, the changes I make are no longer saved.

 

These are mostly inconveniences, but I'd rather have them solved instead of having to spend time before a flight entering a route I fly often or changing the options of that aircraft.

The only thing i can think off is are you running as admin rights and hopefully you didnt reinstall in the default location being the program (86) folder and installed fsx in its own root drive.