I had exactly the same situation as the OP on Sunday evening with BA.

Not wanting to wait till next day for the LHR - CPT in A and LHR_DXB_LHR I thought I may as well take a chance with the regular BA desk. She took the PNR, made the changes and suddenly put me on hold for a few minutes. She then came back and said that this was a RTW ticket and she did not have much experience and was not sure she did it correctly, but has reserved the seats in my name anyway and asked me to call the RTW desk next morning just to confirm. When I checked the manage my booking on BA...these segments did not show up.. so I guess she really did not do it correctly.

Anyway on Monday morning the BA RTW could see the reservations she made and updated the PNR correctly.

I guess I was lucky to find a junior operator as any experienced BA operator would have immediately slammed the phone down upon seeing it was a RTW.
So the moral is to keep trying a few times.