MakerBot Industries

This is a known issue from the Z stepper driver being disabled when it's not moving in the latest firmwares. In the motherboard preferences, you have to check and then uncheck and then re-check the box for hold z. It's a double combination where the firmware has it disabled by default and rep-g might be showing it's enabled. By going through the squence, it ensures the motherboard really is set to hold the z axis. Note HIT apply between changing the settings!!!

Background:
The Z motors are not low inductance/resistance so they tend to generate a lot of heat since are not moving much. In order to combat that, the stepper driver gets disabled between moves. This is a problem because the 8x8 pitch rod can allow the z to slip down between moves (something that didn't happen when using 8x1.25 threaded rod).

Covered in this thread as well.
http://wiki.makerbot.com/forum/t-416181/problem-with-z-axis-positioning
http://wiki.makerbot.com/forum/t-420264/3-1-firmware-z-axis-bug-affects-tom-and-5d-cupcake-shield

Let me add the good news-this means your Z axis bushings are perfectly aligned and the system has very little friction!