The new SCT Bromelton service represents quite a significant expansion in SCT operations and even at 4 days per week ties up a lot of resources across the ground. I'd say as well that a key pressure point for SCT would also be their Laverton Depot. Unlike there new depots, the Laverton Depot (apart from a loop) doesn't lie parallel with the mainline like Parkes, Bromelton, etc. So I'm guessing that requires more setting up of wagons), even though I'm absolutely certain that SCT has an operating regime to manage all of that.
If trains are late on the E-W things like sequencing of locos, crews and many other support services will be quickly out of whack and that would put a strain on turnrounds etc. The other thing is that ARTC (thankfully) have been doing quite a lot of work extending loops on the Adelaide - Melbourne section with new signaling installations etc and that may also have an impact.
Even so if their motive power is suffering a higher than normal number of defects affecting performance then that's not something to be fixed overnight. Their fleet especially the SCT (EMD's) appears to be tightly utilized. I'm not sure how that compares with Aurizon and PN performance of their fleet used on intermodal services E-W and N-S???