NetApp Support does not have any concrete ideas yet.
Looking at the Cisco, in one port-channel we have two interfaces; one is up and passing traffic and the other is down/suspended. On the NetApp e0a is the interface passing traffic and the e0b interface is the one that is linked to the suspended interface on the Cisco. Yesterday we swapped the two cables for e0a and e0b on the NetApp. The interfaces on the Cisco automatically swapped their up/down statuses. This means that the e0b interface on the NetApp is the "bad" port and that the problem really appears to be on the NetApp.
NetApp support is asking for our Cisco configurations today, so we'll see what that leads to.
Thanks for reading along.