tripleback, you should understand that majority of support questions come from users that have never looked at the manual, ever...
remartinez, I am glad that you solved the problem. If you encounter this erratic behavior again, please contact me directly. We would like to know how this happens to duplicate the problem by ourselves.
Anyway, the 'official' Mach3 plugin that will be released in the coming weeks, will almost completely substitute the PoKeys software. We think that it is better to have all the settings in one place to avoid confusion. I don't have details on what the current plugin does with the settings - maybe Scott (poppabear) can answer you here.
Regards,
Matevž, PoLabs