Tunnel Duration refers to the length of time that the WASSP tunnel between the AP and the controller has been established. Control information, statistics, user traffic can all be passed down this tunnel. The AP and Controller have a poll cycle or "heart beat' to determine that the AP is still up and active.
AP Uptime refers the length of time an AP has powered up and actively running.
AP Uptime and Tunnel duration can differ in the event that the AP loses its WASSP tunnel with the controller due to network disruption but stays powered up and continues to service clients.