So I'm assuming that each show's "big loser" is either predetermined or

at least picked more or less randomly so that they all get about an equal number of losses over time.

For one, it's pretty obvious that they film far more encounters with people than they edit into the show. (This is obvious from the outtakes shows, for example.) Say they're in a grocery store having to follow orders for pranks with shoppers. I'd guess that they must do at least 10-15 pranks per joker, where there would be a number of successes and fails, and they pick the funniest/most entertaining bits to edit into the final show, keeping in mind that they need a predesignated joker to fail enough times to be the big loser for that episode, so they'll show more of the clips of that joker failing. Note that sometimes they'll show 2-3 encounters for one joker for some challenge, and only one for the others. That's simply because they have more quality material from that one joker for that challenge.

I noticed a few times that the number of thumbs down didn't add up over the course of a show. There was one, for example, where three of them had one thumbs down after a couple bits, and then after the final bit before the punishment, Joe all of a sudden had three thumbs-downs and was the big loser. I'm pretty sure that sort of thing has happened a few times.

It also helps explain the "joker vs. joker" challenges--they probably just didn't have that much funny material from the other guys' encounters in the situation at hand, and it doesn't matter that it's not "even," because the big loser is predetermined anyway.