In the default abort code I added a gcode for absolute positioning before doing the move to x0, y200. My guess is that it was in relative mode when I aborted.
; Sample stop code - modify to your needs!
M400 ; Wait for current moves to finish, clearing the buffer
M104 T0 S0 ; Disable extruder
M140 S0 ; Disable bed
G90 ; return to absolute positioning
G1 X0 Y200 F9000
M84 ; Disable motor