I'll be using animation shop 3 only.

Open animation shop 3 and click on file then new

Make your width and height 5 for both.

Check Transparent or Opaque, it doesn't matter on this tutorial which one is checked.

Click OK

Zoom is by 5 so you can see what you are doing.

Click on your dropper tool and select a color from the color pallet to the right.

Once you've chosen your first color the click on the brush tool.

Make sure your width is 1

Now draw around the edges till you have something that looks like this

Now select your dropper tool again and select a different color from the color pallet

Now select the flood fill tool and fill the inside of your square with your new color.

Now right click on your picture and duplicate selected until you have 3 frames.

Now select your dropper tool again and select a different color from the color pallet

Select your flood fill tool and click on the outline of box 2

Select the dropper tool again and select yet another color then use the flood fill tool to fill the inside of the box with your newest color

Repeat that for the 3rd box also

Click on View then on animation

Click on file, save as

name it and click save

now you have a pop up box, click customize

on number of colors make sure it is set on 255 colors

click OK

click next 3 times then finish.

This is what mine looks like