I can come up with a number of sanity checks that you could do.
- Ensure that the pitch of the z-axis is correct for your setup.
- Are you setting the z-axis to zero before you start cutting.
- When you are at zero, and your bit is touching your top surface, do you have enough length left in your bit to cut through the wood.
- Please let us know what your setup is. With the classic z-axis setup people have come across challenges where the router runs into the z-axis bracket and cannot go deeper. You can also check if your spring loaded z-axis clip which connects the z-axis with the router is still engaged or is forced to disengage.
Also, not sure how you are cutting, but as a rule of thumb you should not be cutting deeper than the diameter of your bit in a single pass. How many passes have you programmed to run through the bit?
I hope those questions help to get you back on track.