Mach2 or 3 does not use the registry. The "profiles" (all of the settings) are held in an XML file in the MACH3 main folder. Each profile has a different name and is the list of profiles that year presented with on opening the program.
All that being said if you want to preserve offsets there is a check box in Config/State called "Persistant Offsets". Make sure it is checked. There is also an offsets option in Config/Logic that has to do with how offsets are handled at the end of a g-code run (m30 event).