Hello allow me to introduce myself, my name is Drew and I recently started working on a game in RPG2K3 in my spare time. I've had this problem with transparency in tile chipsets that I've tried to import into my project. I noticed a tutorial at
http://www.rpg-palace.com/tutorials/
that deals with this problem, only the tutorial is for RPG XP and does not seem to apply to 2K3.
I'm sorry to bother you guys if this is an old problem, however I browsed through a few topics to see if there was a quick explanation and did not see my answer.
Maybe post a picture of the problem you're having. If it's the same problem the Importing Graphics topic fixes, then opening it in photoshop or even character maker 1999 and doing what the guide says should make it work.