Now I see, I would just make a white layer and then use a pattern to recreate the checkerboard background and make that your bottom layer. The reason its dissapearing is that isnt part of the picture but merly the default transparent background.
You can always make a pattern like the transparent background and then put in on a layer and it will save with the gradient fading to the checkered background.
Thanks guys, appreciate the help and information. Makes sense.