it is possible that the left & right carriages are misaligned, causing slight binding...

to correct - loosen the set screws on the pulleys on the rear rod - work carriages back and forth until it moves smoothly, set carriages near the middle of travel on the Y rods in a neutral position and re-tighten the pulley setscrews being careful to not twist the X axis.

video here: http://wiki.solidoodle.com/belt-adjustment

i was thinking the back rod.

But you said it moves fine with the belt off, so why would you think the back rod?

but ive noticed the Y-axis does not move smoothly, i disconnected the belts and now it moves fine, replaced the belts, and it gets very jerky, disconnected the stepper, still jerky, could it be the rear rod? solidoodle 3

Could it be the idler pulley at the other end of the axis? If it moves fine without belts then that would rule out a rod. All that is left it what is connected when belts are in place. That would be the motor, the idler, and the carriage.