Shinyizer got stuck? Do you mean shinys were just appearing alot more than usual when you stepped on the shinyizer. I never used shinyizer before actually so I'm not quite certain, but I also think there might've...again I'm not too sure, but I belive an error in an event or just something in the rom itself is modifying the variable. Maybe, because I actually looked through some pokemon with YAPE, I found out you added new stones, so I assume, given that in the original advanced games you only had what, 6 evolutionary stones, what you added in with those 6 stones, the way I see it, could be the problem as to what the shinyzer isn't working like it is suppose to.
With my broken shiny encounter spree-thing (where a lot of shinys appeared including Regirock and Registeel), the regular pokemon are fine, but you may want to add to your thread a bug that if the shinyzer like mine did screw up, you should not do legendary events, because I have a funny feeling, if you find another shiny legendary using that broken shinyzer, they are going to be bad eggs.