Have you tried to include the "hidden" segments in your itinerary, in particular the missing SFO-xxx-MAD leg? AA doesn't fly to MAD from SFO, so I assume you're looking at SFO-DFW-MAD or SFO-LAX-MAD or SFO-MIA-MAD or SFO-JFK-MAD, etc? Also is the tool seeing the SYD-SFO service?

With its buggy tool, Oneworld is defaulting to individual airlines and their revenue/tariff departments, and GSAs like Mindpearl, to do the interpretation and brokering on ticket issuance, route verification, etc. As consumers we apparently have no recourse when one of these parties does something counter to the rules; there's no Oneworld policy police to blow the whistle.

I've been trying to find a travel agent in South Africa who could consummate sales of Oneworld RTW tickets but so far I've drawn a blank. I've sent several emails to large-ish TAs in Joburg and Cape Town, and have asked some South African FTers for recommendations, but nothing yet. I will persevere. Meantime, I guess "do your best" and "be patient" are the salient bits of advice.

I also recommend at least trying to use the tool with very limited itineraries, then once the ticket is issued, using the re-issue vehicle, which doesn't have to be handled by the issuing country people, to put it right, even if it costs $125 to do so. (In other words see if you can get the tool to price something like JNB-SYD-LAX-JFK-LHR-JNB, then once issued, populate the rest of the flights through a reissue. Make it easy on the bad robot.)