I thought that your opponent could not shuffle your deck. They can cut, but not shuffle. If they want it shuffled a Judge has to do it. At our last tournament the judges decided to let your opponent shuffle and you can cut after they shuffle. Some people also shuffled everytime during the game instead of just at the beginning such as when I use a seek card they shuffled my deck instead of just cutting it. Isn't there a set rule on this somewhere?

They can shuffle the deck in order to ensure the deck is random. If they are taking too much time doing it, then I would call the judge over. The judge should never touch your deck unless it is for a deck check. Atleast that is how I see it.

But yes, your opponent can cut and shuffle the deck if they think your shuffling was not good enough to make your deck "random".

The opponent has the right to shuffle and or cut the deck any time the deck is looked through, or before duels. So, if you search for a monster with Mystic Tomato, or use Painful Choice, or anything like that, after you're done shuffling, the opponent can then cut or shuffle the deck to ensure its randomization. Most people tend to shuffle the opponents deck only before duels, and after a Fiber Jar Flip, and then cut for everything else in a duel.

I also thought it was illegal for an opponent to shuffle for a while. I think the rule book says you opponent may cut with shuffle in parenthesis. I have to check.

Now I do shuffle my oppoonents deck every chance in tourneyment play. Some people don't mix up the cards enough when they shuffle so I try to make it better.

Something I forgot to mention, but Duelin covered most of it.

You can not just shuffle a deck for no reason. Something has to of happen to allow you to search through the deck. So unless you had a last will, wotbf, sangan, or any other kind of search or deck modifier used, you are never allowed to just shuffle the deck.

What about Reload and Monster Recovery. If I don't look through it do they still get to shuffle? I have tons of cards that make me shuffle.

Painful
Thunder
Shining
Serpentine
Monster Recovery
Reload
Cat of Ill Omen

Any time you shuffle your deck, even if you don't see the the card faces, you are still required to present your Deck to your opponent for additional shuffling/cutting.

Cards like A Cat of Ill Omen do not say "the deck is then shuffled" even though they do allow for a player to go through their deck. Is this on purpose, or should an errata be put out saying: Place the trap card aside and then shuffle your deck. Place the card on top of your now-shuffled deck?

It is normally understood that the deck is shuffled any time a person searches through the deck. I think they are giving players the benefit of a doubt here.

Anytime you search your deck for a card, your deck must be shuffled and or cut.

Like VenomLord, and Bigred Blues stated, any time you see the contents of your deck or mix something into your deck, you MUST shuffle your deck and present it to your opponent for additional shuffling and/or cutting. The ONLY times you wouldn't shuffle your deck after searching your deck or adding to it would be if the card specifically stated, "Afterwards, do not shuffle your Deck."

theres a flaw in your statements guys, for cat of ill omen, if you had to shuffle then the trap will not still be on top of your deck so cat'S effect would be useless

You fetch the card, the Deck is shuffled then the trap Cat of Ill omen got is placed on top of the deck.

If your opponent does not wish you to shuffle his deck, immediately call for a judge to handle the matter. Chances are something fishy is up.

No, ti jo. In the case of Cat of Ill Omen, the player would select the trap card they desire from their deck, and set it aside. Then, they'd shuffle the deck, and give it to the opponent to shuffle/cut. Then, they'd place the trap on top of their deck.