So ignoring the camera entirely for the moment… if you home and laser the same design 2 or 3 times onto the same material how repeatable is the homing? If that is not 100% repeatable then for sure that will affect alignment.
This can be a factor for sure. Also make sure the switches are well secured as well to make sure that the part of the laser that activates the switches is free of debris or other impediment.
You could try reducing the value of $24 (Homing feed, mm/min) which is the speed at which the switches are reactivated for the second time during a cycle. This might improve accuracy.
Else, getting more accurate switches may be required.
Question, when you have applied the X and Y shifts in Camera Control window, are you hitting “Save Settings” after that? If not, those settings are not retained.
Other things to look out for:
Do you have a repeatable resting location for the camera? How is it supported? If you have any slack or spring in that mechanism it can shift things slightly
Focus, camera alignment is only good at one distance between camera and material height. If that distance changes even a small amount this will throw off alignment.
I don’t believe it is either above scenario. Watching the camera live when shutting my enclosure door doesn’t appear to cause the camera to move for example.