I may be doing things wrong, but my FABkit is not calibrating position based on the end (min/max) switches (G28 in CNC mode is supposed to move to the defined home, not move until it hits the end switch), and manual jogging ignores the end (min/max) switches.
First row without pressing anything, second y min is active, check them al this way if they are on the right pin. Check config as well, i had to change home y to other side missing/deleted image from Google+