Upgrading from dopus 8 to 9 I experienced, that toolbars which are
docked at the edge of the screen
hidden (so they appear if you move the mouse to the screen edge)
lost their transparency.
So no matter if you tick transparent or not, they are not transparent anymore.
I played aroung whith all options which seemed to be reasonable, no success.
I can't remember the exact reason but it had something to do with the changes for vista. I think the theory was that if it's hidden it doesn't matter what the transparency is and when it's shown you want to see it anyway so the transparency is fairly pointless.