I think a reason why you can't see the later flights (direct ones on EK) in the evening is that this engine displays a certain maximum number of results ordered by departure time. Obviously this needs to be fixed by EK.

Like Dave said, and mentioned earlier, a quick call to EK will have you on the flights you want. When I searched on EF I put VCE-SYD return just so availability shows up as if the ticket is ex-VCE, which is your case.