Um. That's probably one of my situation too. I am both good at Biology and Chemsitry. However, I prefer Biology over Chemistry (only by 100 times). Then I should go with Biology, shouldn't I? That's where the problem arises - scaling of Biology is low!
At the end of the day, should I choose Chemistry sorely because it has got better scaling? I don't think so. Next year, I will drop Chemistry (wise, wise decision, that is) because your interest must come first.
However, let me ask you. What are the two subjects that baffle your mind? Unless the scaling difference is atrociously high, I wouldn't recommend you to go with the higher scaling subject. If you lack interest, you won't put much effort. HSC is all how long you can sustain your study routine. Choosing boring subject will completely ruin that.
So tell me, what are your subjects? I might be able to give some advices to lead you to the right direction. (hopefully!)