Set both sides to A/A, or set your both sides to 100/F (or 1000/F if it's a Gigabit port)
Duplex is negotiated at the start. When you are using AUTO (A/A), there is negotiation, but when you have manual settings (100/F), no negotiation is taking place from that side!
I.E. Only side with A/A will negotiate duplex.
Negotiation implementation is not very consistent throughout vendors. So i would recommend switching to 100/F or 1000/F whenever you would experience problems.
I think the problem you got was because of switch reload, not because of switch upgrade. It was just luck that port got correct settings in the case before.
