I've only just atarted useing Mach 3 so I'm no expert, but have you settup a new profile? if so you could try the default mill profile as a test to see if the same problems happen, if you havent then it could be Mach trying to overide your changes to the default?

I had all sorts of gremlims when I started, like forgeting to apply or save changes to the settings. Works fine now I'm used to it....