1. You could confirm your beam alignment for that axis by:
A. putting a piece of acrylic in front of your final beam bender and taking a shot at the left side of the table
B. then the right side of the table
C. then see that they line up in the same location. If not in the same location then it is a laser mounting/beam alignment issue
2. You could confirm that your laser beam is hitting in the center of the focus lens by
A. Turn the laser on momentarily and burn a hole into a piece of acrylic and look for the beam to be moving straight down and not at an angle
B. Without moving the laser beam delivery in the X or Y directions, unscrew the nozzle and take a second shot into the acrylic and see if the holes are in the same location. If not in the same location then reflecting off the nozzle
C. With the nozzle screwed on, put a piece of masking tape over the nozzle tip and do a brief laser shot, then remove the masking tape and see that the laser shot is centered in the impression of the circle from the nozzle hole. If not, then adjust the final mirror as needed.
3. If it still is at an angle, then perhaps your gantry (X axis beam) is running at an angle.
A. Measure for square on each side, between the linear rail X axis and Y axis. If not square then, depending upon who you bought it from, there may be adjustment for the mounting.
With a new machine, it is always a good idea to check the calibration of the power supply to ensure that you get a long life from your laser and not premature failure. See http://www.instructables.com/id/How-...ade-CO2-Laser/