Can you provide a network diagram of your setup? I think visually. From what you've explained it would seem that the 3560 is routing between the storage VLAN and others? Or how is the storage connected? Are you using FCOE, ISCSI, or NFS? When this is happening try monitoring the ports on the nexus and the 3560. Then you've see if the 3560 is routing storage packets. If that is the case, I don't think the frame buffers on the 3560 are sufficient for storage traffic. Do you only have 1x 10G connection per host?
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