Turns out that hasn't solved my problem.
I'm getting some type of RF/EMF interference that seems mess up my code from operating properly.
I have recently upgraded all my cables to shielded cables, all cable drains connect to Arduino GND and all stepper motors have the motor chassis grounded back to the high power supply. The Arduino has a separate power supply than the motors.
The motors all have 1000uf cap's on their power connections with shielded cables between the motor and driver(Gecko 210x drivers)and the cable drain is connected to the Arduino GND.
Any thoughts on what to try next, I thought it was just a button problem so do you think I should get the thread moved to the Motors,CNC section?