The only way I get the FMC to function correctly is to enter in all waypoints, VORs, NDBs,etc manually. I first plan a flight via FS Navigator, export to FS9,etc. I print out the flight plan from FS Nav so that I can have all of the waypoints available. Sometimes the FMC doesn't recognize certain waypoints, especially on departure, but I improvise on the departures by seeing what waypoints are showing on the cockpit nav screen. I will enter those from the departure runway into the FMC...in order to get a smoother transition on departure of course.

I will save any of the entered flight plans in the FMC for future use. Since I don't use FS Build, I have to manually entere everything. It is true that the FS9 .pln plans don't agree with CS's FMC. All lat/long's may be correct but the distances are always 8nm between each one in the FMC.

The FMC will not recognize ANY fixes from FS NAV like Fix 01, Fix02,etc, so I ignore those and find any compulsary reporting points like BADGER, HANRY, DUGGS, TOU15,etc. CS's FMC seems to recognize those formats. I've managed several successful flights :)