It might be collision checking.
NX9 does more checking to part geometry in all operation types.
Switching off collision checking might get similar performance to previous versions
Collision Checking is up to you.
If you have a complicated part, with material sticking up, and clamps in the way, and a short tool, and NCM transfer moves set to stay close to the part, then for sure you want the system to check.
If you have a flat part on a vacuum chuck, and all transfer moves at a high clearance plane, and a tool as long as the part is deep, then you might turn it off. Of course, these simple situations where you don't need the checking are the ones that take the least amount of time to calculate.
If you turn off collision checking to save time, I would at least gouge check the path (or the entire program) after generating the tool path.
I don't remember exactly what changed between NX 8.5 and NX 9, but in general, collision checking is getting more accurate and more specific, and there we added different clearances for the tool neck, shank, and holder.