Template question

Hi.

I'm a recent convert to using templates, but I still haven't mastered the art of using them. My most recent venture is the very simple minimovie icon I'm using for this post. To make it, I followed minttea's Adding Movies to Icons tutorial and snagged one of the templates she posted here. To make the base, I magic wanded the two rectangles, one at the right and one at the bottom, and deleted the white space; floodfilled the large square and typed my text; and then saved everything as a gif image. Then I copied it and pasted it in Animation Shop and did pretty much all the steps she listed. However, it would appear that the two rectangles ended up being white instead of transparent, as I'd hoped they would be.

So my question is, can anyone please tell me what I did wrong? What should I have done differently in order to have successfully turned the two rectangular areas in the template transparent?

Thank you very much for any help you can provide. :D