Sounds like you might need to do an Esteps calibration.

Okay, a quick explanation:

The printer motors run in "steps," which are units of rotation.
Inside the printer's controlling CPU are settings that tell the printer how many steps equal one millimeter (steps/mm).

The Esteps for your Z axis motor are off, and need to be re-calibrated.

I'd suggest looking up "E steps calibration." I only really know how to calibrate the Esteps for the extruders myself.

Oh, and you can access your printer's eeprom from the "Devices" drop-down menu in Makerbot Desktop. The button "Device Preferences" is the eeprom settings.

FIRST THOUGH: If you go through with this, please make sure you know exactly what you are doing, if you mess up your eeprom, you could possibly damage your printer.