That's true, but we have filtered the "fake votes" in the past. It just wasn't checked as well this year due to lack of man-power, and some fell through the cracks.
I'm not suggesting a system overhaul, but if three comics end up as finalists in EVERY category, that limits the "real" finalists in many of them to just two. That's really not fun. And what if we have five super popular comics next year that are finalists in every category? They get to be awarded as best sprite comic and best photo comic? Story and strip? Do the judges get to say "no awards at all?" While someone suggested letting panels toss out and replace comics, that too is flawed, because it denies the worthy comics the joy of being announced as a finalist -- and the extra traffic. Plus, a contest where the winners are consistently NOT from the announced list of finalists? I can't imagine that going over well with anyone.
It's not like the comic creators are upset that their comic is a finalist in 5 categories instead of 10 -- if the other categories make no sense, have zero chance of winning, and might unintentionally bias both judges and readers against them (it happens, unfortunately). Some categories can't be "filtered" and I wouldn't suggest it (like humor, writing, romance, etc.), but some categories have really obvious and specific qualifiers. Completed comics must be completed. Sprite comics use sprites. Website design implies some amount of design to it (at the very least a line of code altered from the original template). Charby was nominated as "best photo comic" last year, and NO ONE liked it. Least of all probably Amelius. Those are situations we can prevent without making too much of a judgment call.
--Oh, and we can assure that judgments don't enter into things by providing descriptions/criteria for each category. We have put descriptions up in the forum before, usually when deciding which categories to include for the year. We can put those up somewhere for voters to look at, and when JNP or a couple people go through the ballots, they can follow that filter process of only the ones that simply don't fit criteria AT ALL.
Or we could just announce the top however many comics we have (like any getting more than X number of votes) but still take the five most voted for judging. Call the others runners-up that can move into the judging at the panels' discretion. In any case, I think the comics that we judge should have the honor of being listed as finalists. (However, I still think that our usual attempted minimum filtering in necessary to avoid bad blood. The creators shouldn't get grief for their devoted readers nominating them in ridiculous categories.)
EDIT:
It's funny when I talk about tweaking things people always seem to have such an all-or-nothing attitude! Change isn't always drastic.

If I suggested a room to be painted one shade darker, I'm sure some terrified person would shout "No! We don't want it to be solid black! How will we see!?"
And actually, I wasn't suggesting change at all, just trying to be more on the ball with what we've already been doing. I simply think it most be done a little more carefully for the sake of peoples' feelings. I know if my comic was "popular" I would hate to have it be a subject of contempt or ridicule or one that denied a chance to comics in categories I didn't even fit even if my fans meant well.