Going on the missing DTP packets assumption....
...if you do care to keep trunk negotiation on and the utilization looks normal, you can try checking for line errors and collisions on the trunk ports on both ends of the trunk. Such errors can be caused by a degraded connection (bad hardware) or a duplex mismatch. The duplex mismatch will speciifically cause collisions.
Just a quick note...if you do determine that the speed and duplex settings are mismatched, just set both ends to auto-negotiate. Auto-negotiation sometimes causes a problem, depending on the manufacturer of the hardware and the default behavior of the hardware and drivers, but auto-negotiation for the gigebitethernet standard is pretty robust and defaults to 1000/full on all Catalyst switches anyway.