The IPG tells us that:
“Penalties for decklist errors discovered after the affected player has begun playing his or her match are issued at the start of the next round to minimize the disruption to the match currently being played and provide consistency in case some players have finished playing their match before the penalty can be administered.”

However, in the Annotated IPG, there's this phrase:
“Now, this doesn't apply if you feel the deck is illegal”

So, let's imagine this scenario:

A) R1 has started and you finished counting decklists. Two of the lists have 59 cards. It means, there's a chance that the decks are illegal. The affected players are about to finish G1. Do you wait for the start of next round to do a targeted deckcheck or do a midround one?

The reasons for waiting (consistency) are already listed in the IPG. But, if you wait, you're allowing the player to do another game(s) with a possibly illegal deck. Which one is more damaging to the tournament integrity?

B) What if there was only one 59-card decklist? Is the “consistency” not an issue now? Would you act differently?

I think AIPG's phrase is weird. How one can feel the difference between a decklist-only error and an illegal deck?

1) I would ask both players to find a judge after they finish playing they R1 match and fix lists before R2 starts. They receive their game losses in the beginning of R2 as usual.
2) Judges' decisions should be consistent across multiple events, not one. Thus, it does not matter how many players are there with an illegal decklist, I would stick to “issue penalties at the start on next round”.

Edited Alexey Chernyshov (Nov. 5, 2015 05:14:38 AM)

Difference here is between player listing 59 decklist but playing with 60 cards deck (issue penalty at the beginning of next round) or player using 59 card deck as well or having listed illegal cards (issue penalty now). Easiest way to find out which situation we deal with is just to interrupt players for a half a minute and count their decks. If indeed they are illegal (59) issue penalty, if not, have a judge nearby that will direct them to judge station after the match is over. I would go with that solution no matter if it apply only to one or both players in match (that is unlikely)

Also, remember that AIPG might not be up to date due to recently judge wiki downtime.

Looking at the current IPG on Wizards website I cant find that phrase anywhere in the IPG.

Here's what I found on the Oct 22nd 2015 IPG

Penalties for decklist errors discovered during a deckcheck and deck errors are issued immediately. Other decklist penalties are issued at the start of the next round to minimize the disruption to the match currently being played and provide consistency in case some players have finished playing their match before the penalty can be administered.

EDIT: added IPG date

Edited Elliot Garner (Nov. 5, 2015 09:44:16 AM)

Originally posted by Jorge Monteiro:

R1 has started and you finished counting decklists.

Why are you counting deck lists, instead of being on the floor, helping players?

d:^D

Let's be nice and assume that Jorge meant "R1 has started and you finished verifying all decklists are present" ;)

Originally posted by Dustin De Leeuw:

Let's be nice and assume that Jorge meant “R1 has started and you finished verifying all decklists are present” ;)

LOL! Asking *me* to “play nice”… :)
(Hint: not happening)

Actually, this is exactly my point: if we've only verified the presence of one list for every player, then we have no idea that there's a 59-card list (or two). However, we might still discover that, at some point during the event. And when we do, we apply the penalty at the start of the next round. Unless, of course, our review of that list leads us to believe the deck itself is illegal, in which case we proceed as Bartłomiej described.

A bit of TL;DR: one of the goals of this shift in philosophy is to stop expending so much effort just to detect simple, clerical errors. Counting all deck lists does not greatly improve the chance of catching a cheater or other serious problems; it does, however, put too much emphasis on clerical accuracy. The fact that it also takes judges off the floor, where they can provide customer service, just tips the scales further.

d:^D

I think almost all 59-card decklists I have seen have been paired with 60-card decks. If I were presented with a 59-card decklist, I don't assume that the deck is incorrect, I would wait for the following round. I would also wait for ambiguous card names (“Jace” in Modern).

One of the few scenarios where from a decklist alone I would assume the deck is illegal is an illegal card for the format (for reference: I've seen this exactly twice).