Some of the transformations preserve partial transparency (like resize) but some don't (like enlarge canvas and pasting a copied image). Also, it doesn't seem possible to reposition the image when enlarging the canvas.
Oh, thanks for pointing that out.
Some effect by default will convert from any image format to GIF format.. partially for transparency reasons.
We're working to improve PNG support throughout our effects.
Canvas resize was just updated to support PNG transparency.
I'll look into other ways of scaling the canvas.