Somehow I've expected this, after I have tear apart my patch srcipt in the latest days.
Currently I'm working on a overhaul of my script.
From what I see, at least the error is a double file definition, comes and the "game/animations_and_flags.rpy" file comes from a previous version.
You must delete it, as well as other files:
If it won't work then I would recommand a new installation with the upcoming 0.12.1 from Runey. You don't need to transfer your saves as they are in a separate place (at least for the Windows version).