What kind of Z axis motor do you have? The original machines were shipped with a SEM Z axis motor. There was an upgrade to a Parvex motor which was stronger. The drive was also changed to a stronger one.
What is the serial number of your machine?
What version of software are you running?
X axis homing in a different place is because the marker pulse on the X axis motor encoder occurs at the same time as the X home switch making. Move the home dog for the X axis so it will be seen sooner. about .030 inches should be enough.