In one of my templates, I have set the vertical margin of the module's container to 5px, and the bottom border to 5px, colour #FFFABA00. Top, left and right border widths are 0px.
When I save and close the template, and then open it again, the vertical margin is always reset to 0, and the border is missing too, so I have to set them over and over again.
I am using version 3.1.0.5249.