MakerBot Industries

You get the same answer as the other guy with the cupcake and skipping

I have calibrated the stepper drivers for the old NEMA 17 motors

But you haven't replaced the old and very inadequate motor which is the problem so that's why it doesn't work.

I know Makerbot has had them out of stock but if you send them a support message of how much trouble you've had, maybe they will sell you just one for Z, although honestly, you really need to replace the x and Y as well. $21 each and problem solved. http://store.makerbot.com/nema-17-stepper-motor.html

Or, get these http://ultimachine.com/content/kysan-1124090-nema-17-stepper-motor
which will only fit for the x and Z motors on a cupcake, but those are also the 2 motors most likely to skip (because Y axis is the lightest and least drag). These motors need the REF voltage to be around 3.0-3.2 volts (2 volts =1 amp, so 3 volts =1.5 amps). They are rated nearly 5 times as much torque as your current motor because they are physically bigger and are also low inductance.