Try to calibrate the machine over the longest distance you can so that any errors are as small as possible. I normally set the machine to zero and run it as far as I can and simply measure with a tape, check the travelled distance and alter it if required and test again. I did my Z axis with a dial guage and steel rule. Good enough for me. I wouldnt have thought that the machine would expand or contract enough to cause any movement. I have checked some of our big machines at work during warm summers and winters when its regularly below zero and the machines are always inside 1mm over a distance of 10mts.
Have you checked over the mechanics to rule out any backlash?

Regards

Ian