Maybe you can try Soft Reseting, sometimes it helps. Good luck.
ive got 5 shinies all in the advance version no cheating devices usedtry to get abra/dratini its the easiest buy 5 at the game corner and check then soft reset
You haven't been playing the games since the early days of Gold and Silver I presume.
Oh and btw, I didn't count in the pre-set shiny Gyarados in the 2nd Generation games.
Trying to remember which shinies I've seen and when:
Heracross - Gold
Weedle - Gold
Magnemite - Crystal
and ironicly:
Magnemite - Sapphire
Deoxys - Emerald (although I gotta admit that I used a cheating device to encounter lots of Deoxys for it's EV points. One of them were yellow.)