Hi Mike,
That does sound like a STP problem.
Does 'show spanning-tree blocked ports' show that any of the channel ports are blocking (at either end) ?
And 'show etherchannel port-channel' shows 2 ports in the bundle and both up ?
Thats the kind of thing i would expect to see if the channel was not operating correctly, in which case STP would block one port.
Cheers
Shaun