I installed Mach3, ran through the conconfiguration to get it set up and everything worked great. Then I loaded Bobcad  into the computor. I designed a part, converted it to gcode and tried to start the mill when I found out that it no longer worked. The X Y &Z all seem to be loaded in the same port. the X axis goes in the same direction regardless if I manually press left or right, the y axis only works when I press the Z key.
Did the computor reconfigure itself? Help!!!

Sounds like your xml got corrupt or possibly you started a different profile.
Try using the restore settings option from the Operator menu.
Hood

After you configured it did you select Save Config at teh end of the config menu?

It can be a real pain at times, but if you completely screw up your config and don't select Save config it means that all you have to do is restart Mach3 to get back your machine.

There are a few other places where you have to do something similar, but it is really done that way so you have to deliberately save stuff that will alter your machines behaviour.

After you configured it did you select Save Config at teh end of the config menu?

It can be a real pain at times, but if you completely screw up your config and don't select Save config it means that all you have to do is restart Mach3 to get back your machine.

There are a few other places where you have to do something similar, but it is really done that way so you have to deliberately save stuff that will alter your machines behaviour.

Afraid thats not quite true, Mach will (or should)  save any changes you make to the xml when you shut Mach down correctly, no need to use Save Config. It is however a good practice to get into and actually in Rev 4 you will not be able to do anything at all in Mach until you have chosen to save after changing config settings.

Hood

Thanks for the advise.

I tried using the restore button, which reboots the computor. When I bring it up, the reset light is flashing. I click on the the reset button, but it will not reset. I tried pushing in the red emergency stop button, but that did not help either.

Sounds like you will need to re-do your settings. This time make a copy of the xml  just in case things go wrong again.
Hood