Homeing after bed transform applied bug fixed in the duet branch.  The master branch will be updated after some further testing.  The problem was the X endstop.  If X is homed, that stop is triggered.  Homeing Y then only moves Y, and so only the Y endstop is tested.  But when the transform is applied X moves slightly when Y is homed (as it should) and the X endstop stoped the movement prematurely.  You will need to update the files on the SD card as well as the firmware to activate the fix.