Delta printer printing incorrect dimensions in X and Y directions. Z dimensions are correct
As detailed at minow.blogspot.com (which I found very helpful for the most part - it was the first link in the answer to my related question) you need to check/adjust the zero in front of each tower, check the zero in the center, tweak the radius, and repeat (checking the zeros at the edge of the bed in front of each tower again) until it's correct. 

After that you adjust the rod length to correct XY size (and recheck all 4 zeros, thus the radius - it makes for a less than exciting day, but is worth it in the long run.) 

You either need to turn off EEPROM until you have the right settings, or save the setting to EEPROM each time - depends how worried you are about using up EEPROM write cycles, I guess.

You should also turn off auto-bed-levelling while getting the basic calibration correct, per the same blog instructions.

My fun with figuring out what my EEPROM was doing behind my back is here:
Delta printer not responding to changes in DELTA_RADIUS