I agree mostly with Dustin, although Nicola (and Phillip) made some good points as well. Here's my opinion:
In this case, it seems pretty obvious that the judge who did the first deck check made a mistake. The judge (as I understand the situation) did not even think to check that there were some extra cards there and see what they were. In this case, the judge is in the wrong and the player is in the right; the judge did not do a thorough deck check, should have noticed the problem, and notified the player that this was illegal behaviour and assessed that as part of the first DDLP. Given the situation as it stands, I would not give a second penalty.
However, as both Nicola and Phillip pointed out, there is room for abuse here. Here is my proposed fix: When doing a deck check, if there are extra contents of the deck box, look at them and see what they are. It should take a whole extra 10, maybe 15 seconds of your time. All you need to check is “are any of these extra contents Magic cards?” You do not even need to check what cards they are. If there are extra cards among the contents of the box, notify the player that he should not keep extra cards in his box as part of assessing the DDLP. Then the player knows about the issue. The next time that player gets a deck check, if he continues to have those cards in his box, and if the situation requires (the cards are legal in the format, they are playable in the player's deck, etc), then a second DDLP can be assessed, because by notifying the player of the problem the first time, you have shifted the blame from “judge made a mistake” to “player is rebellious”. If the player uses the “I didn't know, the judge never told me” excuse, it's easy enough to find the judge who did the deck check, ask him if he notified the player, and say “Sorry, player, I asked the judge, he said he did tell you, and now your simple GL for DDLP has been upgraded to a DQ for Lying to a Tournament Official. You also may be investigated for UC - Cheating. Have a nice day”.
Edited Lyle Waldman (July 7, 2013 03:50:14 PM)