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I don't think the FWSM supports NetFlow; AFAIK it's only supported on ASAs.
I had the same issues within our network. Currently the FWSM does not support Netflow at all. The only method of extraction of Netflow data from your core switch / FWSM is using a collector like NProbe or FProbe. It takes Span traffic (mirror port) and converts to Netflow data that can be pasted to SW. I have it setup and its giving amazing information about our network.
Here is the write up from a recent thwack post: Orion NTA and nProbe: Analyzing bandwidth hogs without flow-capable network equipment
Hope that helps