I'm afraid that at this point it's complicated to fix things: I didn't know this IRV system and many users probably didn't know it either, I actually had to look it up on Wikipedia to see what it was. And since the rules simply ask you to vote up to 5 pizzas, that is what people will do.
I don't think that its so complicated to fix it as all that is needed is for icopress to just add a short explanation and then people can simply edit their votes.
In that case all those who voted in numerical order should be contacted via PM to inform them about this rule. But I'm not sure people will actually pay attention to the rules because I see users with almost no merits voting anyway, and as we can see people keep voting in numerical order, this is the last one for example:
I vote for: #39, #50, #57, #73, #87
Maybe Xal0lex actually wanted to vote in that exact order, it's possible, but do you believe it? The most natural thing is to write down the numbers and submit them, if you want to make a preference list than you need to double check all the numbers to see which pizza is the most and least favorite.
In my opinion this system is overcomplicated for this type of contest and it penalizes the pizzas with the highest number (and what I'm saying goes against my own interest because my number is not that high).