There are too many variables here. If you add some more information it will give someone a greater chance of helping you.
What IOS/CATOS version are you running on the 6509 switches? Hybrid or native mode? Are all the switches running the same version?
What version of Orion and NTA are you running?
What version of NetFlow are you running on the 6509? NTA only supports version 5 with NTA V3 supporting version 9.