Layer shift after Filament change (M600 with Marlin)

[3dprntz 4]

I'm trying to understand what happened on my Ultimaker Original that when i used the Cura filament change post-processing gcode that it shifted about an additional 1-1.5 mm on the X and Y axis. The firmware has M600 or advance pause enabled and went through all the steps for filament change. I heard that the motor turns off during pause on timeout, but i didnt touch it and it seems like it was software or firmware. I did set the script to go X0 Y0 and X 2mm above the print. Should there have been a homing before it returned to the print after the filament change? Or am I missing something in the firmware?

 

Thanks!