When you shuffle your deck in manner of just turning couple of cards from one side to another, the deck will come in almost the same order before shuffling. I mtg it's forbidden, and penalty for that is either game loss or dissqualification if doing so on purpose (cheating).
I use the MTG method for malifaux as well. Two people shuffle their own decks. Then each other present another the decks, and they can shuffle. After that you can shuffle again, but then the opponent must do shuffling of your deck as well. Then if you cut the deck, your opponent get to do the same on your deck afterwards. So before the start of the game, your opponent must be the last person who touched your deck.
Shuffle half of the deck into another half and always ask your opponent to shuffle his deck, to do in that manner, if you see he is just turning cards from one end to another. The whole point of it is to have fun, so if you find cheaters don't hesitate and use all you come to think off to mock him for that.