This thread is intriquing me as I was helping another user earlier today, who has a K40 that is exhibiting similar, but not identical symptoms. Unfortunately we have not found a solution there either.
I just downloaded and checked your files. Your SVG, PDF and the top half of your AI file, align perfectly. Your AI file however contains a second set of the same graphics and they are slightly misaligned. Although not nearly as much as your results on the laser. I’m convinced that problem is caused by the erratic movement of your gantry. Now, why it’s doing that is yet to be determined.
This is the other thread. I pointed her here as well, thinking maybe something common would reveal itself.