Covert changed the layout of the sprite sheets in the MC 1.4.x versions, so textures made for them won't work. Fortunately I figured this may cause issues when I textured that, so the fix for this particular problem is easy, just go to the railcraft/textures folder, and delete the "gui_coke_oven.png". Now rename "gui_coke_oven_NEWVERSION.png" to "gui_coke_oven.png", and everything should be peachy :)