Another thing to keep in mind about the C3KX-SM-10G is that it only allows you to collect NetFlow data about traffic that traverses the uplink ports on the module. You still can't get port-to-port NetFlow data if the traffic doesn't cross the service module ports.
One other solution is to port-mirror your traffic to a NetFlow probe. Do a Thwack search for "nProbe"; some people have implemented that successfully with NTA. Netfort might also work; I'm not sure.