OK, a few things, the train in question is the Hansen Quarry train, previously known as the Apex Quarry train. Hansen are unrelated to Boral.
The train runs twice daily to Kilmore East, where it is loaded with crushed rock.
The first train departs Kilmore East in the Early afternoon and runs via Albion to Hansen's Brooklyn facility, usually arriving at Brooklyn at about 1600, but sometimes earlier, sometimes later.
After being unloaded at Brooklyn, it returns empty to Kilmore East (again via Albion) usually arriving at Kilmore East at around 2130 from memory, here it is loaded again.
The next journey is dictated by demand, it will either return to Brooklyn as above, or it will run to Westall, making the journey from Kilmore East to Westall in the dead of night via Essendon where it will park up for the night, before being unloaded in the morning, and then returning to Kilmore East in the mid to late morning, running via Essendon.
It is unrelated to level crossing works, and does not carry railway ballast (this is collected from the Boral quarry in Deer Park, using the old siding next to the new Caroline Springs station currently under construction).
There is also talk in another thread that PN may be loosing this contract which could shake things up a bit.