This is the second time I have seen this question and I while I do not know the answer for sure you would have to think that packets that are ONLY L2 switched that never cross a L3 interface would not have netflows built for it.
But I am sick of wondering I will find out today for sure and post back today if no one else does.
I've seen this question before too. I think it has to do with IOS version and the version of PFC card you have in the 6500. According to Cisco, if you have a PFC3A card, you can only collect NetFlow stats on routed traffic. You need a PFC3B or PFC3BXL to get layer 2 data. You also need to be running IOS 12.2(18)SXE or later code.
See the NetFlow Overview section in this document:
Hope this helps!