There are some bitmap functions that just don’t work in UE3’s implementation of Flash. I guess you found another one.
I think you’re going to have to desaturate the image in UnrealScript and draw it to the canvas.
Or you could make a desaturated copy of every possible texture, and in your Scaleform movie put the desaturated copy under the color copy, and make the color copy visible/invisible to toggle between them.