Hey, when swapping from the Carbide pin to any endmill the bitsetter has been setting the depth too deep by 0.004 or more. I have been setting the Z both manually and with the Bitzero to confirm it wasn’t that and it only happens when I set zero with the Carbide pin and then swap into another endmill.
Zero is set to bottom happens with more than one type of endmill
CM642 latest. CC 778
If you have the C3D router make sure it is powered off. Insert a bit or the pin and grab hold of it and see if it moves around. The Makita/C3D router bearings go out on a regular basis and that could be the source of your problem. If the router bit wiggles you will have to rebuild your router or replace it. The rebuild kits are available and takes some mechanical skill but is not too bad.
If the router is not the source double check that your BitSetter is firmly mounted. The bottom of the C3D pin is rounded but a regular bit is more or less flat on the bottom. That could also be the issue. The shape of a bit may depress the BitSetter differently over the pin.
It is like the old joke. A man goes to the doctor and says it hurts when I raise my arm up. The doctor replies “Dont do that”. So maybe stick with a bit to set your depth and not the pin. As long as the bit or the pin are consistent stick with what works.