Make sure you don't have any loops in your connection to the switch...if you're using LAG between switches or router to switch, ensure that the LAG configuration is using the correct ports or the switch will disable any ports that are causing looping. Generally your switch will indicate whether it's blocking a port due to loop detection, so that one is more obvious and you likely ruled that out already.

If the switch is showing packets flowing through the port(s) you think might be disabled, it could be the device on the other end of the cable causing the problems. Try turning off "green ethernet" or "energy saving" ethernet in the driver of the devices (especially if they are Windows systems) as the driver sometimes doesn't handle energy-saving e-net properly. I've seen this happen a handful of times.