British Airways Comair
Unreasonable excess baggage charge

I flew from London to Cape Town via Frankfurt and Johannesburg. On the first 2 legs of the flight I was able to take my hand bag and small box with guitar equipment as hand luggage. The small box fitted in the overhead lockers without any problems.

When checking in in Johannesburg, the check in lady wouldn't allow me to take what she claimed to be 2 items as hand luggage. Surely my hand bag doesn't count as my hand luggage?
I was forced to check the small box in under fragile and was told to pay R350.

I think this is totally unreasonable as this wasn't an issue during the first 2 legs of my flight and should be allowed on as hand luggage as it only weighs 8kg.

I would appreciate some response in this regard and would hope I will be refunded for this unjustified cost.