I too am having trouble with my Lulzbot Mini. It used to print mechanical parts that had 0.5 mm clearance just fine, but now those prints don’t fit together. I don’t know the answer, but the Slic3r page on dimensional errors has given me a few good hints: http://manual.slic3r.org/troubleshooting/dimension-errors.
I noticed on my latest prints that the inner walls of objects seem wobbly - so I’m looking at a few things: belt tension, bed auto-leveling (that’s another story), and extruder idler screws’ tension. I’ve recently found the extruder idler screws’ tension can make surprising difference in the quality of the print.
Update September 10: I seem to have fixed the problem (or at least a significant part of it). First, my right X carriage height was about 1/8" lower than the left, so I turned off the printer and manually turned the right screw until the two X carriage mounts were at the same height from the top of the printer. Then I found that Slic3r page on dimensional errors, and it got me thinking about the ripples I’d seen sometimes in the first layer. I then adjusted the extruder idler tension, the ripples disappeared, and now the printer prints parts that fit together fine!
My complete notes on adjusting the extruder idler tension on my Lulzbot Mini are at https://bluepapertech.com/3d-printing/extruder-gear-tension-the-overlooked-adjustment/