Irfan,
Attached is a screenshot of the motortuning dialog, which is where you change the direction pre-change. I agree, it's weird that it's only one axis, perhaps you damaged something while switching cabinets. ESD damages sometimes shows very strange symptoms. Bypassing the BOB and then swapping drives should tell you.
Another thing to try could be to swap the motors between X and Y, does the problem stay on the Y-axis or does it follow the motor? Swap the step and direction signals between the BOB and the drives, is the problem still on Y although the signals now goes thru what used to be the circuitry for X etc...