So I was doing some cleaning on my L-Trac-X Trackball w/2 extra jacks, 800 to 3200 CPI, which i have been having roughness problems with. No matter what I did i had a lot of stepping and sometimes when moving the ball from rest it would have more resistance in a certain direction than another. Anyway, I was doing the cleaning and had just the right light to notice on one of the three metal rollers an odd spot. Taking a closer look I noticed that a small spot on the roller looked as if it had been filed flat. /facepalm
How I missed this after two months of of cleaning and use is beyond me, guess I am just not a very anal person when it comes to small details. Now I shall order a replacement roller and bask in the smoothness for all eternity.
TLDR: Filed flat spot on one of the metal rollers that I never noticed.