Hi Dan, yes I have had this exact problem! It's not the alpine windows, windscreen or aircon drains. The short of it is that the water leaks into the heater box plenum when there is heavy rain. It can be a bitch of a job to fix, but if you're patient you can do it yourself. It's actually a design fault that allows the water to run down the windscreen and into the heater intake.
I see you're in Sydney, so I can't show you where/how to fix it sorry. You need to remove the lower windscreen trim that sits behind the wiper arms and fashion a water diverter that is glued above the heater intake. This forces the water to run either side of the heater intake rather than into it.
Bear in mind that the trim is difficult to remove. If you are not very careful you can crack the bottom of the screen where the 2 retaining feet hook under the screen.