I'm not sure that I understand what has been done.
When running axis Y with Gecko Z was Gecko Z completely replacing Gecko Y or were just the motor and encoder cables switched from GeckoY to Gecko Z?
What is the setting of the Current trim pot on Gecko Y?
Are you absolutely positively sure that the encoder or power cables have not been switched Pos to Neg. Having them reversed will prompt an immediate fault when the Gecko attempts to turn the motor.
Notice that in the Gecko directions the Red is Neg and Black is Pos
Wouldn't it be nice if that were the problem?
Good luck!