Can you do a show ip flow inter command. I don't have a machine here with subinterfaces but this might show us something. Also can you take a PCAP from the NTA server? It will show what interfaces are being exported.
When I execute a "show ip flow interface" the result shows the LAN interface where the sub-interfaces are created from:
ip route-cache flow
If I apply ip route-cache flow or ip flow ingress/ip flow egress, that covers all sub-interfaces associated with the physical interface.
What's a PCAP?
BTW, Netflow settings is set to "Enable automatic addition of NetFlow sources".
Sorry for the acronym - PCAP is a packet capture. If you load Wireshark and capture packets on the NTA server we can see what the sources are sending. That will tell us if the issue is with the source exporter or NTA. Wireshark is freeware.
This might vary based on IOS version but on my 2800s and 3800s, in order to receive Netflow data from subinterfaces, I've had to add the ip route-cache flow or ip flow ingress/egress statements to the individual subinterfaces I want flow data from. Just something you might try to see if it helps in your environment.