Joe, you say you replaced the operator panel. Check the wiring that goes from the op panel to mainboard for any shorts or pinched wiring. If this is okay, then it would seem to me that the phantom command to autofocus is coming from the mainboard and not the control panel. I don't know if you can inhibit z-axis by breaking a wire to the plunger circuit - I will check if I have any info on this.
An erroneous command could originate on the mainboard due to noise issues or even bad layout. You probably don't want to change mainboards for this. If you want to get this running inexpensively, what I would suggest is to figure out how you can disable the z-stepper motor after the job is focused, just prior to running the job.
Suppose that you could add a switch to lock-out the z-motor functionality during lasering. Then it can't autofocus on it's own during lasering. The trick is finding out where you can add the lockout switch. I don't think you can add it to the motor winding itself (load) as switching windings open is usually bad on the motor driver. But if you can get some schematics or a tech to help maybe you can find a place to add a switch to inhibit z-axis motion. (On the motor power side?) If you wired it like a lid-switch, you could focus with lid open, and it would lock-out z-axis with lid closed. (This would be okay, correct?)