Pictures of the setup and results might help diagnose, but it sounds like the headstock and tailstock aren't perfectly aligned. Put sharply pointed centers in each and, with the quill fully retracted, push the tailstock to the headstock until the centers just touch. Are they perfectly point to point? Back the tailstock up and extend the quill untill the centers just touch. Are they perfectly aligned? Differences between the two tests point to certain issues, too. Could be adjustments necessary in either headstock or tailstock (or both), or the ways are uneven, warped, or twisted. Have you checked the ways for level in all directions? Just a few things to get you started.