No, AFX is for both FS9 and FSX, you can switch between versions when you open up the program. I read some posts though over at SimForums and see that this is a problem with other developers of scenery, they are indicating that AFX connections are much more "finnicky" in that the connecting points must match exactly, if anything is not matched precisely, then it shows as a fault.
Regardless, I downloaded the old version of AFCAD and sure enough, no faults, just as you posted. Now that IS weird.
Thanks for the reply, keep up the good work.
John