maul_inc: Unfortunately, something is different with 1.1 and since Hayden (the author) only owns the steam version he has trouble making the tool work for the GOG & retail versions.
So as of now, you need the steam version for the tool to work with witcher 2 1.1. I'm sad :-(
That is indeed unfortunate. I've just read it, as I haven't even gotten to this point.
For me the flawlessws.exe itself just shuts down right after starting it. Flawless my arse :)