Etherchannel should not be killed by spanning tree , the channel is looked upon as 1 link and thus 1 side would "not" get shut down. Look at the utilization on the link and see if it is high , also look for any errors on each end . Make sure the link config is set the same on both ends . If you hardcode the speed and duplex on one end , hardcode it on the other end also. Do you see any dropped ping responses across the link ????