Without any material mounted, can you jog your Z axis so that the end of the bit touches the the waste board - aka zero the Z at the top of the waste/spoil board.
If you cannot jog the bit to touch the waste board then you’re at the end of your Z travel where the bit stops. What happens when you try to continue to move the Z axis downward is the belt skip; you’ll hear a clicking type sound but the bit won’t move downward. The controller believes the bit has moved because it sent the signal to the servos, but due to physical limitations it won’t. When you attempt to go back to 0 it will move the bit higher than expected as the controller thought it was lower than the bit actually was.
Do you have a Makita of DeWalt router? the Makitas are a bit shorter and probably run into this issue.
Your options if you are at the end of travel are to add another piece of sacrificial wood under your piece, or extend the bit out of the collet more. I’d recommend adding another piece of sacrificial wood depending on bit size/length. More length out of the collet increases run-out and chance of breaking a bit.