Hi Dave!
You might be experiencing accuracy problems. Try to set the config.pro option enable_absolute_accuracy to Yes and change the CATIA reference part, your MFG assembly and workpiece to absolute accuracy (0.005mm) - They all must have the same accuracy. Then try again.
If the above not work, try to do the same but also export the CATIA model with a smaller tolerance. (You have to set this in CATIA)
Some material about accuracy in Pro/NC