There are a couple of other issues with the software - it doesn't seem to remember any of my settings (in the plasma screen) between sessions - I have to manually enter them each time - not a big deal - I guess this could be due to it being a dev version.
No, that is not because it is a dev version. It shouldn't be doing that. Not sure why yours would be. Can't repeat it here. If you started with a clean install and the default profile and screen I see no reason for it. If you have anything custom start looking at that.
The THC module creates the registers and sets the relative ones to persistent. You should be able to launch Mach, set all the variables, close Mach and launch Mach again and all the variables should be whatever you set the variables to in the last session. If that isn't happening you have a problem unique to your setup. Custom script, screen, corrupt machine profile, antivirus, etc.
Sometimes the program stops after a pierce saying the a the OB motor took to long to move - 4 seconds (I'm para-phrasing here - I do not have the exact error message)... seems to happen after about 20 or so profiles in a single file. Agh - lots a messing about trying to reset/re-start the program and trying not to lose position.
When it does this look on the Machine Diagnostics tab. What does it say machine state (little lower than midway down on left side) is?
You can also try to make the the time longer by adjusting the Diagnostic, Regfile, iRegs0/nf/thc/MoveTimer value. 4 is the default value and stands for roughly 4 seconds. Try it at 8.