First discrepancy I found was the first search I ran (LHR - SYD one way Mon 3/11) but I'll try to give a more helpful general case answer.
- Consolidators [that you don't have commercial relationships with] have wholesale arrangements with airlines allowing them to sell tickets below the direct/GDS price. I suspect you're more reliant on ITA results than many other portals or meta-search sites and their prices are trivially easy to beat on competitive routes if you have a broader range of partnerships.
- Some consolidators put together logical itineraries not bookable via GDS or even direct with the airline. As an extreme example I once bought a cheap, logical pair of connecting long haul flights with Saudia via eBookers that Saudia's website wouldn't allow me to book at any price direct with them; I'd guess the airline didn't want to market anything involving a 5 hour layover in an under-redevelopment terminal in Riyadh. There are plenty of less glaringly obvious potential indirect itineraries that consolidators (potentially including Kayak as well as their affiliates) can identify with Innovata's minimum connect time file and schedule data[1] and other providers might have a more liberal view on reasonable connections than ITA
- Sometimes other sites' metasearch results' advantages are purely illusory, based on outdated results they've cached or screenscraped. I find Skyscanner LCC prices are frequently out of date, even though the actual ticket price is also usually cheaper than ITA's. Other sites might also create the appearance of more choice by not combining codeshared flights into one.
As for LON-SYD on Monday Kayak has a lot more results under $1000 than you. It's possible their much cheaper ticket prices with SIA are outdated or geolocation specific, but the cheapest flight they show (a Garuda two-stopper that's no more obviously agonising than your cheapest result but 10% cheaper) doesn't show on your engine at all. Then again, the price with Kayak had risen to only 5% cheaper than your best price when I started the booking process...
[1]disclosure: I sell that data, amongst many other things, although not to OTAs