There are two kinds of overtravel alarms. One is the alarm generated by the OT switches, and there is a switch for each direction in each axis. If one of those switches is actuated, the OT alarm happens and you can only jog that axis in one direction (away from the switch). The other kind of alarm is a SOFTWARE overtravel, which only happens on Fanucs that have "memory" on their axis position. Later model Fanucs have either absolute encoders on the motors, or encoders with a battery backup. These controls can remember where they are even if you turn off the power. On those controls, you may power up and find that you can hit a software overtravel even before you perform a "Zero return" on that axis. Older Fanucs without axis position memory don't know where they are until you zero-return after a power-up.
I'm assuming that your control is an early 0M without memory on the axis position, so when the control is turned on it has no idea where it is. On those controls, the zero-return function works like this:
1) You jog at least an inch or so away from the home position
2) You turn on the Zero-Return switch and jog towards the home position
3) The axis moves in rapid until it hits the zero return switch (a cam switch)
4) The axis slows down and continues to move until the cam switch drops off again
5) The motor stops when the pulse coder hits the "1-turn per rev." pulse
6) The zero-return light comes on for that axis, and the control "knows" where it is.
7) If software OT limits are used, they become effective as soon as you zero-return.
Notice that you can hit the hardware OT switch if the zero-return (cam) switch sticks in the "on" position. It must turn on, then DROP OFF for the zero return to work.
Also, if the drop-off point of the cam switch is TOO CLOSE to the OT switch, that would mean that the cam switch drops off, but the pulse coder can't make one full turn to fine the "1-pulse per rev." signal before hitting the OT switch.
Note that there are also some parameters to "shift" the zero return position by up to +/- one turn of the motor. This parameter can also cause trouble if it is set wrong. I'm assuming that no one messed with your parameters before this problem occurred.
Removing and reinstalling the motor (if the pulse coder is in the motor) or removing and reinstalling a separate type pulse coder can cause the "1-pulse per rev." signal to shift positions, so this problem frequently happens after a motor replacement, etc.
If you have batteries on your pulse coders, and you're getting a SOFTWARE overtravel alarm, move all three axis to the middle of their travel, turn off the control, hold the CAN and the letter "P" key in at the same time, then power up the the control. That will cancel out the software OT protection until you zero-return all 3 axes again.