You should never...
...Use more than one code at the same time (for instance, berry max and TM max).
...Save while gameshark is on with codes enabled.
...Save without turning off Gameshark and checking each menu (including Pokemon Stats and Bag sub-compartments) for glitches.
Using a Gameshark is an iffy thing. You managed to successfully catch all of the Pokemon without messing up your game, which probably took quite a while, just to lose it all because you weren't careful with the 'Shark. From one victim to another, BETTER LUCK NEXT TIME.
P.S. Work smarter, not harder.