Different cut depths during 2 stage carve

I have completed a 2 stage carve involving raised letters and recessed background. The rough cut Z was set up with the probe. After changing to the detailed bit, I once again set the Z with the probe. The detailed cut around the letters went deeper that the rough cut by what by what appears to be one to many passes by the the detailed cut. The board was flat and the deeper detailed cut depth was evident around all the letters. Is there G-code variables that can be checked and changed to correct the difference. Thanks in advance - Fred