Yes, I checked the PC boxes. I also knew in the back of my mind that I had not received them because I just got the shiny Entei wonder cards two weeks ago and had only picked it up in Heart Gold and Soul Silver. I am not sure if this is a true glitch or if my friend corrupted his game with the action replay. Regular gameplay goes on without problems, so I was not sure if that was the case. Is there a way to figure this out without checking for bugs with items or pokemon stats/movesets one by one? I have not deleted the wonder cards as of yet. I have until 8P.M. (EST) to make my decision, and if I were to sacrifice one of them just to have more time to tinker with this and still get the shiny Suicune, it would be the shiny Pichu one. I thought resetting might fix the problem for a new game, but as you said, I figured that if there is something wrong, it would not necessarily vanish by starting the game over. I thought mixing records might resynch some coding or do something similar to the patch for Ruby/Sapphire that came with Emerald. I will try it and see if it does anything once I get off work.
I actually don't know much about action replay or the save editing programs. Again, I have the actual wonder cards from the event. I know I could hack it in the worst case scenario (once I learned how to do this), but I would rather use the event cards I went to the stores to get. Stubbornness aside, it feels like a waste.