Our company recently discovered this loss as well. If you research the help function of Microsoft Picture Manager it tells you
You cannot make your pictures transparent using Picture Manager.
For a broad range of editing options when working with pictures, the best approach is to work with a photo editing program, such as Microsoft Digital Image Pro
Imagine that. That is a $50 piece of software
I did find a freeware program called GIFFY that will make a single color transparent in a GIF image
http://www.emu8086.com/giffy
That may help you out if you cannot purchase an alternative product