On the two routes that you detailed Virgin Australia does not have any of its own flights.
However it has a codeshare agreement with Singapore Airlines on those two routes, which means you could purchase a VA flight and not travel on a Va plane.
I did a quick check on the VA website and the codeshare flights are shown.
Kayak uses matrix ita, but also pulls fare data from over 400 sites, so it is likely that VA have not offered that fare grouping to ita, but is offering it on its own system, or through another partner.
Kayak case study (from ita website)
Kayak.com, the largest Travel 2.0 site in the world, is a global Internet media company operating Kayak.com, Sidestep.com, TravelPost.com and TravelSearch.com. Kayak.com and SideStep.com display results from more than 400 travel sites, providing prices and itineraries for hundreds of airlines.....
(There is more to this quote but I think it covers what I want to say)