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LDave, is this a layer 2 or layer 3 interface?
I assume the export is configured the same for all of the interfaces on this switch. You could try to shutdown and re-enable the interface to make sure it picked up the changes to the flow configuration (obviously you would need to do that in a maintenance window).
To see if the problem is with the device or NTA, you could run wireshark and see if flows are coming from that device. The filter is 'cflow' and you'll want to limit the traffic from that one source. You'll also need to know the interface id to find the right flows (from NPM go to the Interface Details page for that interface and you will see the interface index number).
Sorry for the delay I've made few tests with our network guy and we managed to solve the problem.
I had to add the related vlan under nta monitoring and not the physical port of the core. This is related to the fact that our building uses a different type of connection towards the core than the building in which the core is present.
Your mention of wireshark and the hint to look for the interface id helped me to narrow down the boundaries of the problem, so thank you.