Without knowing how you have your router set up, it's kind of hard to answer your question. I have run into something similar before and depending on your setup, there are a couple of things that might be causing your issue. First off, do you have CEF enabled on your router? If not, I believe you'll need to enable it to see all of the flow data.
Secondly, are you using subinterfaces on your router? If so, you'll need to put the ip route-cache flow or ip flow ingress or ip flow egress statements on the subinterface. You'll also want to make sure that you are monitoring the subinterfaces in Orion, otherwise you'll get messages in your Orion Event viewer telling you there is a missing NetFlow interface for your router.
Hope this helps. If you have any other questions, just let me know.