If a 50 W laser cannot cut through 3 mm acrylic in one pass, something is badly wrong. Messing with the Z-axis cannot improve the situation: you must determine the actual problem and fix it.
Some areas to examine:
- Is the lens properly focused on the material?
- What cut speeds & powers are you using?
- Have you verified the mirror and lens alignment?
- Is the tube lasing in TEM00 mode?