Ok, step by step.
1) open your game folder
2) open Graphics
3) open Characters
4) find the character spriteset files that are causing the problem
5) move them into any other folder
6) run RMXP and open your project
7) left from the testplay button in the toolbar at the top of the window (on the right half of the screen) is something called resource manager, open it
8) click Import
9) browse for the character spritesets your just moved out of the Characters folder
10) click on them and open them that way
11) click on "Transparent color" and choose the visible background of the file
12) click OK and you are done
@oneray: Here you go. I put a Readme file in there, so you know what to do. Just download the attachment of this post.