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.