Make sure that the laser lines cross in the center of the rotating disk. If they don't, you might want to adjust the lasers appropriately by truing its knob.Right. But doing this literally tilts the lasers.
|Outward flay example.|
The scanning problems could be solved with a calibration wizard like Horus has. Horus has it's problems, like the fact that it doesn't finish the mesh like the Rubicon software does. But Horus is open source! The Rubicon guys should take it's calibration and save themselves some time. Or maybe they should take what they've done, add it to the Horus project and use it, and make everyone's scanning better! It would do a lot to improve the longevity of their project as well. Makerbot was built on open source software, and fell when they abandoned it. Just sayin'.
As it is, at this point I'm considering either modding the scanner with 3D printed lasers holders that are adjustable, though that will never be at the right angle for the software's assumptions either, or just tear it down and build myself a ciclop from the parts.