It sounds like the Z rods that MakerBot ships with are inferior and possibly should be replaced to get a fully functioning makerbot. On my kit, version 11, I have rebuilt the Z stage assembly several times and keep it excessively well oiled to prevent slipping. Essentially, the problem is that the rods are slightly bent and also corrode which adds friction. Replacing them with stainless steel equivalents seems to solve these problems. For now I am running a software patch that slows down the Z axis to reduce the odds of lost steps during a build.