This is very odd for this to do this.
When your E-stop or limit switchs are activated does it cut the power to the motors in anyway? You DO NOT WANT to cut the power to the motors OR drives on the DC side of the circuit. This will cause voltage to climb, or have no place to go and burn drives. When cutting the power it should be done on the A/C side of the power supply so that the DC circuit is still connected.
What type power supply do you have? It should have big capaitors and even some type of resistor that bleeds the capasitors after power is shut down. These motors put voltage back into the system when they coast, even if the power is shut down. If there is no place for this voltage to go burning drives, or even motors is what can happen. Your every lucky blowing fuses is all that has happened no matter what the cause. You need to fugure this out. Of course I understand that is what your trying to do here but just to let you know this can cause big problems.
The action that your system takes when the E-stop or limit switches are activated is very critical, this is what the guys mean by needing more info on how you have your system wired and setup. The complete system, not just the limit switchs. So a detialed description of your wiring of all systems might help the guys figure your problem out before something gets beyound repair. The fact it only does this on some drives is bit odd. WIthout knowing any wiring of system info I would say check all connections on the DC side of your motors and drives. A connection that was lose and not making perfect contact could aid in causing this, but expect something else to be the cause.
Good Luck
Jess