So after doing my calibrations I changed the m665 and m666 lines in config.g to the following. Now I find that a home all on the first boot up does not move the y axis at all. If I stop it and press home all again they will all move OK and after a single calibration I get prints I'm very happy with.
M665 R81.51 L160.0 B75 H177.02 ; set delta radius, diagonal rod length, printable radius and homed height
M666 X-0.13 Y-0.39 Z0.52 ; put your endstop adjustments here
When I revert back to the original config I don't get the Y axis funniness but I do have to calibrate 3 or so times to get acceptable prints.