If you are doing the cut at the same time as the engrave, you can get 100% perfect alignment accuracy by doing the alignment in your design software before you print it.
Discussion on it below:
It should only get out of alignment if you are trying to use visual alignment to engrave on something that has already been cut out.
Also…have you run the Camera Calibration and do you use the Set Focus tool? Those will help with the visual alignment issues.
