Thanks to jighead81 and his keen eyes for noticing that the IN and OUT labels on the silkscreen layer of the new FatPants 2012 board are swapped! I've made a note of this in the documentation and corrected the silk layer for the single sided layout. It's too late to make the correction on the manufactured board, unfortunately.
Just remember- IN and OUT wires need to be reversed for the manufactured PCB. The Single Sided version has been corrected.
So sorry :)
Corrected doc:
http://www.madbeanpedals.com/projects/FatPants/docs/FatPants.pdf