[/B]Firstly, welcome, and secondly, you need to read the not so fine print. The T&C's of the voucher spell out quite clearly that the voucher only covers the base fare and not the fees and taxes that are collected in addition to the base fare. Granted, things could be a lot simpler, but I suspect QF don't want to be out of pocket for the 10x bonus point offer and are banking on the fact that many vouchers will remain unused and simply expire.
In Victoria, you will find that VCAT will make findings against such prohibitive restrictions because it enables unlawful enrichment, so you can seek recourse, if you can be bothered.
As for your situation, the $392 increase in fare is based on the fact that the booking engine locates the nearest base fare that exceeds the value of the voucher as it will assume you do not want to "forfeit" any value, despite the next lowest fare potentially being only a few dollars less. Id call telesales, explain the situation, and you may get a cheaper fare and forfeit a small amount. Otherwise, and don't quote me on this, you could try buying a return J fare between mel and syd, cancel it and put the value into (regular) credit and then use this credit for your CNS-MEL purchase, as I don't THINK QF would credit the value back to a voucher. Wouldn't hurt to ask them the question I suppose.