I know, I know -- one would think that in Q3 2014 there would be very few links in an enterprise (of any size!) that weren't using auto-negotiate, but I have some customers from a previous life that insisted on hard-coding everything! The result, as you can suspect, was a boatload of odd network performance issues that were only found while on the device itself.
Auto-negotiate is often the cause of the duplex mismatch messages. Many times equipment from the different or even the same vendor will not neg full duplex.
Yes, hard-code EVERYTHING on the network, because ambiguity in technology implementation leads to the same sort of problem as it does in conversations, both parties assume incorrectly, about 40% of the time.
Silly rabbit, duplex mismatch is for kids!
Peter