We are running ether-channel between two pairs of 7200 routers, 12.3(8)T code and 3560 switches at out Internet border. When either router is down, application traffic passes fine. When both routers are up and HSRP, OSPF and BGP are not communicating between the routers, application traffic is fine. Once the routing protocols and HSRP begins working, the applications stop working.
The applications worked fine on sub-interfaces prior to creating the port-channels.
With the port-channels and routing in place, everything works correctly from the network point of view (standby correct, ospf neighbors and routing tables correct, bgp looks good, can do sub-interface pings, etc). However, as stated earlier, the applications running over this network stop working or, at best, work intermittently.