Ok... First here is an image of what I get when I render all layers:



This is the house and the ground:



And here are the flowers I put there just to try things out:



I saved the last two images as tga:s, and when I put them together in photoshop I get this result:



As you can see it doesn't look the same as the first image which Maya rendered. Am I missing something obvious? I tried the matte-thingy you explained, but I noticed no difference. I don't know exactly what it does, but when I changed the texture of the outer wall of the house (the red) it turned completly black. The flowers looked the same after...

Edit: Wait a minute... It looks like the flowers caught some of the blue background... Am I on the right track here?