Are you using the tool database and tool offsets? Each tool should be set up in the database with an offset relative to a referencing tool or probe. I used a 1/2" round bar with a point machined on one end for referencing. Once the machine is referenced using the referencing tool, after a tool change Mach applies the offsets for that tool. I never zeroed the Z with an actual cutting tool, always the referencing tool.
I sold the router a couple years ago and don't have the tool change macros that I used anymore, but I think it's all in the Mach manual. Look at the G-code section for tool change and tool offset code.