What is wrong with my Pokemon Emerald(berry issue)?

I am still wondering what about my game is wrong. I have continuously picked berries throughout the game, including very valuable ones, such as the one that Scott gives after lots of wins. Also, I have noticed other errors in this game, where if you go play certain games, the pokemon in your last slot disappears or turns into a bad egg. I am also a heavy cheater, as I have Steelix with eruption, water spout, earthquake, and Meteor Mash, and also many other pokemon, all mxed out and with moves it is not supposed to learn. They are also all shiny. Since bad eggs come from cheating, can this problem be that too? But what cheat specifically should I abstain from?