ST-V2 5 Axis BOB clone, 2 different machines have recently failed enable high

I have a knee mill and a lathe controlled by the same LinuxCNC machine. Recently I noticed the lathe was enabling the steppers on startup. I think this resulted in burning up one of my closed loop steppers. 

Lathe has 2 steppers, rotary encoder and I just finished setting up pwm spindle control. BOB is only connected to PC through LPT cable. 
It has a 36V PSU with buck converted to 12V to power the BOB. The 12V has a second buck converter to 5V connected to PC , PCG. I confirmed on the lathe that the LPT port (disconnected) is setting pin 14 correctly, but I am always getting 5V on pin 14 of BOB. 

I ended up rewiring to pin 16 for the 2 drivers to get it back online. Now I am concerned that I will just keep burning out output pins.

The knee mill drives a relay off the enable pin that controls the stepper driver power supply. Recently I noticed the relay was always on but thought I had diagnosed it to the relay and not the input signal. 

Mill has 5 steppers, 48V PSU for drivers, PC PSU 12V and 5V connected to BOB 12V and 5V respectively.

I went to replace the relay for the mill and discovered it is the same problem. Pin 14 on the BOB is always high, now. It was working correctly before.

Both configurations share a common MPG handwheel and they are connected via 9805 chip and (2) SD-PEX10005 LPT cards.

What could cause these boards to fail in this way?

Any pointers appreciated, I am running out of parts and really need to be making things.

 

Please clarify "burning up one of my closed loop steppers. "
What does that mean?

A stepper being on won't damage it. 

Excessive voltage into a stepper drive input may damage it.  E.g. 12v into a step/dir pin that is only meant to take 5v

I haven't checked the current yet but I suspect it was too high, the stepper was very hot and no longer works. If the enable pin had gone low, the stepper wouldn't have current running through it all day. Both of these machines are new builds.