Forgot to mention that a bad cable is possible on the X pulse coder too. These cables usually flex a lot as the X axis moves, so look for a place where the x cable flexes the most and see if you can "trigger" the alarm when the control just sitting there and on. If the alarm always happens when you zero out the axis, it might be that the cable is flexing just right to open up a broken wire inside the cable.
That one would be harder to fix. I'd recommend just buying a new cable rather than trying to find the break in the old one.