Thanks for the reply's everyone. This is a DIY Machine 1500mmx1500mm using C Beam extrusions, .5" aluminum plates, ball screws and linear rail on all axes. I have 2 48V power supply's running drivers and motors with the Spark Concepts CNC x-PRO V4. I'm not using the on board drivers on the board, but external drivers. I have found out that my motors are pretty high inductance (9.0), so I plan on replacing these, but since it's only one side of the Y axis having problems, I wouldn't think it's a problem with power?
The gantry is square to the machine, have checked it numerous times.
The screws do seem to run very smoothly when not engaged. I have taken the gantry off and I can run the screws up and down very easily. I have also unbolted the gantry from the screws and can push to gantry from one end to the other with one finger.
I think I will try switching the motors and see if the left side has a problem? I think this will tell me if it's mechanical or electronic.