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Legend!

Is there any reason why the rpg maker sheets don't contain everything in the sized sheets?

You could use photoshop or gimp to do this. Set up a grid that's 48x48 with snapping on, move over the parts that you do need, and delete the parts you don't. Funny enough I noticed today that the RPG maker sheets don't contain everything on them, which is a little strange.

Are you using the tiles from the RPG maker file, or are you using the ones in the size folders? In the main file, there is a folder for RPG maker tiles as RPG maker I think works differently from other engine software.  Try using those and that should solve your problem. 

Thanks, I just had the same problem as well.