I figured out the Zekrom/Darkrai issue, as I had chosen the wrong game where they came from, but Mew and a Gyrados are still having problems for me. I'll upload them later today when I get a chance and post back.
I'm having an issue with a couple of event Pokemon, which I don't understand. My Mew from the Fall 2010 event, Darkrai from Winter 2011 event, Darkrai from May 2012 event, and Zekrom from Spring 2012. Anyone else having issues with these?