Easiest thing to do would be to switch the wires on the X and Y axis, at the board, to see if the problem switches to the new axis (look into the board connector or the mosfet/stepper driver on that axis), or if the problem remains on the X (X stepper motor or X wiring).
The stepper motor has two wire pairs, they are: Black & Green and Red & Blue. The resistances of each wire pair should be between ~2.5 and ~3.2 Ohm.
Sometimes the endstops can cause weird axis movement, so use the M119 command in the Pronterface terminal window to check the current endstop status. Send the command twice for each axis, once while open and once while activated.
If you’d like more assistance, please feel free to send in a message to firstname.lastname@example.org, with your order number, serial number, contact information and shipping address.