It's a tricky one to explain so I'm just going to upload a picture. The transparency on the planes for some reason blocks the fur but, paint effects act if the plane isn't there. Rendering using mental ray, but maya does the same thing.
It sounds like your PNG image might not be quite right....Remember, not all PNG images are created equal. Make sure your image has a proper alpha channel (perhaps try a targa format and create a proper alpha channel) but in photoshop, you must create an alpha channel for the image. Make sure you are using a solid black background behind the image if needed, and most of the time I try and keep the background transparent when I save out to a PNG. Technically, black is supposed to render out transparent in a PNG but it's not always the case. You can render out the Paint effects seperately with Maya Software Render and compsite later but it's best to convert the Paint effects stroke to Polygons when using Mental Ray for Renders. That said, perhaps you can post your original PNG image for us to examine. OK? Hope that helps.