I have posted a few messages on this and have finally found the culprit.
We have been experiencing input queue drops on all of our 6500 Fast Ethernet Interfaces that are in dot1q trunking mode. All links have low utilisation and there are no Input Buffer issues.
We monitored traffic on our Access Layer Switches (2950s) going across the uplink to the 6500 and found the switch to be sending Ethernet Test Configuration Protocol messages (an ethernet control frame). If VLAN 1 was removed from the trunk link (both sides) the 6500 would drop the packet, but the 2950 would still send the frame.
Input queue drops would only stop if we added VLAN 1 back onto the trunk link. So it seems that this is either a software bug, or the 6500 switch will only accept the frame if it is received on VLAN 1. We were hoping to use VLAN 1 minimisation across our network, but we need all our interfaces to be clean from errors for troublehooting purposes.
Has anyone else come across this or a work around that will still allow us to remove VLAN 1 ?