It sounds to me like Y has some misalignment on your linear slides and the problem is purely physical.
Or maybe you need to orient your machine so the Earth's magnetic field is properly oriented to the magnetics of the steppers.
Have you tried adjusting the VFD for that axis, to reduce the harmonics?
Have you tried sliding that axis around with the stepper disconnected, to sample the tight spots?
Would you like to get some suggestions that were remotely related to your setup?
Tell us what steppers, what controller board, what power supply, what software, if you've used a voltmeter to check or you're just guessing, WHAT you're working with, please.