We've been troubleshooting with the laser cutter and working with Illustrator in Windows, instead of sending our files through CAD in ubuntu.
Our first problem was working with a file that was exactly the size of the laser cutter bed. The laser was set to auto focus, and while attempting to focus, it would start cutting (We even focused it ourselves, and that didn't work). So we scaled the file's dimensions down just a bit, and that was solved.
With that problem over, sending the file from Illustrator has proven to be a bad idea. The laser is on throughout the entire process when cutting lines, therefore cutting through our piece when not wanted. It seems that the path sent from Illustrator is missing some information to tell the cutter when to turn on and off.
Our solution was to change the file format to a PDF. That ensured that the laser cut only where we instructed it to. We still had some problems; it didn't cut through everywhere we wanted. We by-passed that, by creating a new file, in which everything that was already cut in the 1st pass was deleted. Then we would send this new file, with only what hasn't been cut as a 2nd pass, and that worked.
Phew... still having problems... will update...