If the water tiles work fine and the others don't, then that sounds like you're using the right sizes but likely have the tilesets in the wrong slots. RPGMaker has a weird system that expects tiles to be set up in a specific way: tileA2, A3, tileB, etc. The sets should work if you arrange them based on the tiletype in the filename. If you need more help send me an email with some specific examples of how they look in your game then I'll know for sure the problem.
thanks!