From what you describe, my guess is that you have a corrupt .xml.
If I am right (50/50 chance)...
You could either create a new profile (not as a clone of the original) and configure it (port & Pins etc.) from scratch.
or
Look in your Mach3 xmlbackups folder and choose a fairly recent (before the problem was noticed) one from there ( copy it, rename it to [your profile].xml and copy it into the Mach3 folder - backup your existing [your profile].xml from the Mach3 folder first, just to be safe)
Tweakie.