If you were flying without restriction prior to swapping batteries, maybe you did not update the Firmware on the second battery last time around, and there is a conflict?
It is true what everyone above says about logging in etc., but if the firmware/app updates with the new NFZ are not compatible across the board you may be restricted. When you charged up the battery that was working w/o problems, and tested again, were you still limited to 100ft - or did it work as it has in the past?
If you recharged and no issue, then I would stick batt2 in the bird - fire up DJIGO and see if it thinks it needs to do a firmware update on the battery.