In CS6 if you liquify a transparent layer (e.g. with a few hand painted brush lines) the layer comes back from liquify brigther/strokes seem thinner and also is strangely distorted around the edges of the area liquified....
I am having a similar problem, using CS6 Extended - If I liquify an area with transparent pixels, a rectangular area appears after render, that is lighter than the original. Change in brightness it seems. Does not happen in CS5, same MacPro. Is this a bug?
try holding down the option key when launching Liquify.
this launches it in non GPU mode (or something like that) - same as CS5.
if your video card isn't supported the new CS6 Liquify will cause artifacts.