I have seen this issue on a few machines. In all these cases the spindle had a twist in the splined section. The spindle and quill assembly moves freely where the spline is not bent but when the twisted section tries to go through, it cannot due to a lack of clearance. The best way to verify this is to unlock the back gear lever. As the spindle goes down it will drag the splined gear hub and bull gear down with it.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)