OK OK OK I got really lost reading this thread it seems to me that either you guys are trying to make a GTS sever of your own or are having problems getting om to the Nintendo GTS sever.
Easy the one answer is they are LEGENDARY POKEMON they have different things that apply to them so they don't really count because they are a special case. Also red gyarados is a rare like 1 in a million chance pokemon to catch after you catch it in Lake of Rage.
make sure you enter the right Hex numbers and used the right type of nature
http://projectpokemon.org/forums/showthread.php?218-~Guide-to-44h-45h-46h-47h-and-85h-Values~
just finishing them up right now. My Uncle came up to see my GF and his well idea of visiting is knocking down your front door and then drinking alot of beer hahahahahah the beer part not the part about him knocking down my front door