Passingbay,
Maybe you are seeking advice from the wrong quarters. Perhaps a nicely worded letter to the operations team in the CASA regional office in Darwin would be a better place to seek some clarity on this situation. Although casa won't give a hoot about what rates they charge at this school, wording to the tune of
"and upon receipt of my training invoice, I noticed significant discrepancies between the actual and recorded flight times. When I questioned this with Mr ****, he responded by telling that he knew a lot of chief pilots on this airport, a statement which I took to be thinly veiled threat to my future employment prospects and wellbeing.... can you advise me what actions I should take to ensure that my employment is not compromised in this fashion.... etc etc "
Just may trigger some action in the form of a little talk to your resident idiot IFR tutor. This is after all how (you say) he responded. Expose him for the nasty little grub he is I reckon.