WELL.
I've been messing around with the tool a little more, and I found out something. If there's a costume that was hexed incorrectly, the SD Media Launcher WILL lock up. I don't know why, or what sets it off. I noticed, however, that a majority of costumes hexed with libertyernie's KirbyTool program have a much higher tendency to freeze up the game. I used a Kirby hexed with it; it froze. I rehexed that Kirby by hand, I can now play as him. (Sorry, mate. >: )
Samus seems to freeze the game alot, so does Roy and Peach in general. Mostly characters with a lot of textures (save Ganondorf). I was using my NES Peach, which froze the game; I replaced her with the original costume and now things don't freeze up as often.
I'll get back to you on that, though. It could've been coincidence.