OK. It will an AA flight no JFK-LAX and then QF flight number LAX-SYD. As AA is first flight it will default to an AA ticket. But QF have a single flight number QF108 JFK-SYD. This saves 1 flight segment over JFK-LAX-SYD. May be an availability issue for L class JFK-SYD. Try a different day

MM is not 100% perfect, but usually interprets the rules correctly.
What airports are you putting in the OW tool?
What airports does the OW tool show you?

You need to phone AA to make sure you book direct. Ask for the "RTW desk"