I sent the following message to Nicalis last night:
"I recently acquired Cave Story Wii after the updated version went up, and it has been a blast so far. However, I encountered a vexing oddity tonight that refuses to go away. When I loaded Cave Story tonight, the main character had the red of his hat and pants replaced with a very dark - nearly black - navi blue; afterwards, when I loaded up my save file, he was suddenly the same way in that as well. Up until now his hat and pants had been red colored, the save had been made just before you go into to the desert area. Nothing I could do could get this to stop, I have even deleted both the game and save file along the way numerous times already. So far, once it started doing this, the main character only appears in his correct outfit colors on all copies of the game I have installed if I don't create a save file at all (but you can't really play without a save file). Do you have any idea what I can do to remedy this?"
I got this reponse this morning:
"You actually haven't encountered a glitch, but a trick (or treat) we put in for fans. The main character is getting ready for Halloween.
Sorry if it has caused you some confusion."
*head hit floor repeatedly*
So, basically, I freaked out and deleted my save over a time sensitive Easter Egg (this only works if you redownloaded the game after they updated it on the 18th of this month).