don't know if you got this figured out or not, I see the post was a while ago.
auto QOS isn't configurable on etherchannel interfaces. What you have to do is build the etherchannel and once the interfaces are in the etherchannel, build and apply a service policy.
Ran into this with a recent deployment with 6500s and 4500s with sup7s. There is a pretty good explanation in the medianet campus qos guide that I followed and it worked like a champ. It has specific sections for platforms, and I pretty much just followed the example.