Rounding works on all prizes, regardless of type, but is mostly intended for prizes that are designated as a percentage of the pot.
When prize values are determined, the software first calculates each prize amount (prize pool times each prize's percentage). Then rounding is applied to each prize. The rounding done is exactly what the user sets it to be: rounded up to the next N, rounded down to the next N, or rounded to the nearest N. [Or not rounded at all.]
After doing this, the prize amounts might total to greater (or less than) the prize pool. This is just a consequence of rounding. How to fix this? Fixing this is done by subjectively taking some amount from some prize(s), or adding some amount to some prize(s). AKA "moving the money around." Key word here is "subjective". The software really knows very little about your prizes, and programming the software to "move the money around" would not be subjective, it would be a lot closer to "arbitrary". If the software were to do this, inevitably there would be complaints that it "should take the money from THIS prize, or THAT prize, etc", because the software just doesn't have enough information to make this kind of determination *for* the user. So it doesn't do it. That is left as an exercise for the user.
adhawkins: You don't need to go back and change the prizes to a "fixed" amount just to deal with this issue. You can either (a) adjust the amount of one or more of the prizes (the "Adjust by" field takes a positive or negative amount); or (b) override the amount
tandemrx: who knows? Most likely when I was testing this feature I was changing fields in that file and unfortunately failed to change one of them back before being released. I did notice this sometime back and fixed it, however. Not that it's a huge deal. As you pointed out, anyone can edit the file.