As far as I can see, JogUnitsMode is always set to imperial following configuration of Mach4. JogMode is likewise set to continuous. These do not appear in machine.ini, however, so are perhaps defaults within the core. Flushing, saving, or re-loading profiles is not going to help.
The problem is that scripts are unaware of these changes. Yet they could easely take steps to re-initialise if a suitable signal were provided to indicate the potential need for this.
I tend to side with Robert on this one in thinking that this is an unfortunate feature of Mach4, if not an outright bug.
For now, the best remedy is to restart Mach4 after configuration, whether or not changes were made.
Allan