Like I said before to give us some detailed pics of inside the control box and better more detailed explanation of exactly whats happening and we will get you working.
If you go into the mach3 folder, usually on C: drive named mach3. Look for a file ending (.XML) with the same name as the profile you load ie: MachMill.xml then Zip it up and post here I can load your settings into mach3 and see how it's setup.
Then from the pics might be able to work out whats going wrong.