Hardware: MacBook Pro (2010) 2.53 Intel Core i5 / 4GB RAM
Software: OSX Snow Leopard. Only scrivener 2.0 is running. Menubar / background programs are quicksilver, dropbox, gmail.
Occasionally after exiting full screen mode in Scrivener 2.0 by pressing the esc key, the dock becomes transparent and there are no icons in it. Often, getting back into full screen and exiting again solves the problem.
My dock is NOT on auto-hide
Could you please take a look at the console the next time this happens (~/Applications/Utilities/Console.app)? I’ve never heard of this happening - it sounds as though your machine is having some weird problems switching between the system modes responsible for hiding and showing the Dock.
FYI: I noticed this too but only in the earliest 2.0 versions. It has not repeated since I downloaded the 6076 version. It was associated (for me) with the auto back up bug.