Of the two modes "trunk" is safest. It starts life with the expectation their might be spanning tree packets, while "access"mode starts life wit the assumption their wont be.
So I think I would tend to lean towards trunk mode in this case.
Next the VLAN mismatch errors. This suggest to me the MS is receiving spanning tree or CDP or LLDP packets from something to be able to detect a VLAN mismatch.
I would do a packet capture of one type of packet at a time and then see what you can discover about the over end of the cable. This might also reveal what the VLAN configuration should be.
The MS will tell you what clients are on its ports. Perhaps you could determine where one of these clients are, and then trace back from that client to find out what that plugs into.