I figured it out bro thanks. I remeber messing with some of the settings and opening the thing that lets you view the box.
Also I WAS having the same problem you were make sure the pokemon.ekx was made on the same version of PKHeX so when you go to load the injectiondebug.bin its loaded on the same version as what you created the pokemon.ekx on.
i dont know 100% what fixed it but what i do know is i just got the newest version from here
http://projectpokemon.org/forums/showthread.php?36986-PKHeX-%28Gen-6-SAV-PKX-Editor%29
i assume its safe to post links to the same website lol.