Well, I got around to trying it on another computer, and I successfully injected the Smeargle as a Smeargle 2.
But, then I tried it again to make sure it wasn't a fluke, and it stayed a Zekrom. The name, moves, and stats and such were all transferred, just the species didn't change. No idea what went wrong that time.
Anyway, I'll keep looking into it and let you know what I find out.
Edit: I just injected several other pokemon, and they all worked fine. Also, I don't know if this is relevant or not, but the pokemon I got to work were all edited from a Thundurus.pkm instead of Zekrom. The only real difference between the two computers is that one is XP and one is Windows 7, but I don't know that that would be causing any errors.