Do they not show in the editor, or when youre in MaLa?
If its in the editor then its prolly a 90° issue (like loadman said) or a path problem. When I got the 90° thing wrong in the editor, I would get my text colors and all showing up with my boxes in the correct relative spot, but no pics.
If its in MaLa itself, then you need to tinker in the Layout tab. Maybe you dont have everything placed in a single layout folder? If its just MAME and one layout, you prolly shouldnt be using tree, BTW. Especially if youre just figuring this stuff out.