Hi Earl --
I am not sure we have enough information to fully diagnose the problem. No matter, it sounds like your machine is loosing steps. If the Z-axis is binding and/or slipping when moving up it would "think" that it has reached a higher elevation than it has. Subsequently, it would tend to travel farther down than needed, causing it to go too deep.
You need to check z-axis travel in both directions. If upward travel is stiff or binds at particular locations that might indicate your problem. Make sure there is no debris on the rails, bearings and gears.
Another area to check is the set screw on the stepper motor drive. If it has loosened it could be slipping. Unless you are using a z-axis counter-balance system (mentioned in other Zenbot related threads here) pressure is unequal on z-axis travel. That means the stepper is working harder to move the Colt router up than it is when moving it down, which could contribute to the problem you are seeing.
It would be helpful to know just which model Zenbot you are using, and exactly what you mean about having modified the X & Y travel on your system. Normally, you could electrically swap the axes to determine if a 'lost step' problem travels from one axes to another. That probably isn't needed in your case but it can be useful if an axis drive is suspected as the fault.
HTH.
--Rich