Agree it looks like CS is getting reset when loading new firmware. I wonder if this might be an Axe-Edit issue as well.
I always set my CS to 'All Off' because of how I am using CS system to send midi, and each time I change Axe-Edit to a new preset, then go to controllers, it 'refreshes' all of the CS boxes from Last to Off. I did have to reset all to off (again) after loading FW5b2.