For several years I have struggled with variable backlash on my Y axis. I've torn apart, rebuilt, replaced ballbearings in the nut, extended, moved the stepper to the rear and many other mods thinking that eventually I'd come across a combination of mods that would stabilize my Y. Most recently I finished the Y extension mod and moved the stepper to the rear. Things seemed pretty good but slowly backlash started creeping in: 0.010" backlash. I tried adjusting the gib but no amount of adjustment (basically a full turn of the front and back gib adjusting screws) even made a difference. So I finally decided to tear things down and figure out what the heck is going on. It didn't take too long to figure out as you can see by the attached photos. Even though I machined the ball nut mount to Hoss' Phase 2 specs (the mount is 2.00" tall) I've always had this situation where the mount sits lower in the saddle slot and the lock screws are actually exposed. It's always been like this and I really never thought much about it - stupid me! As you can see, the lock screws have distorted the top of the mount so I can imagine that it is not held anywhere near as secure as it should. It also explains - I think - the variability and degeneration I've experienced. Ironically, tightening the gib would probably make things worse as more force would be required to move the saddle/table and that would result in "flex" of the ball nut mount.
So I'm machining a new mount on my X2 now and I'll make it about 2-3/16" tall so it reaches to the top of the slot and provides enough meat for the set screws to lock it into place. I'm really hoping this has been my nemesis these past couple of years! At least it seems like a smoking gun.