The only thing that was new was Link2SD ( works great by the way). I also went through wiping, formatting and reinstalling the ROM and Gapps. No new apps and when I would change the dockbar action buttons and in the settings menu I would get the ADW FC.
Could it possibly be the SD Card? When I made the 2nd partition for Links2SD I still had things on it like the ROM, Titanium backup etc.