I believe the problem lies with new features in Filemaker 13.
We had that problem recently as one of us tested FMA 13 while most of our users are still using FM 12 client. In FM 13, layouts do have a general background color (Inspector -> Appearance) which does not exist in FM 12.
It seems that when you edit a layout in FM 13, you might accidentally set this background color which then takes precedence over the elements' background colors you can manage in FM12.
So, the solution is to open the layout in FM13 and set or remove this layout background color.
You can see that "Layout background" feature on the right side of the image below. (source : http://www.technologytell.com/apple/131237/filemaker-pro-13-for-os-x-review/ )