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Hi,
Does anyone know why a loaded profile would have reverted all its settings values to 0?
Software Version: 1.2047

Blank or 0? The 2 things are not the same!
If talking about basic/standard DROs, (e.g. an axis velocity value) the value goes 0 on startup if the value for the DRO saved in the profile file is 0.
Or if the screenset it limiting the value for the field.
E.g. if the maximum value of a DRO is set to 5 and you want to write 10 to it then it will still have a value of 5, because the screenset setting limits the max. value to 5.

I'm talking about pin assignment for each axis such as step pin and port, direction pin and port etc. The values are 0. They are not blank.

The machine is moving again after assigning the axes pin values. I also set the E stop pins. Now I want to get back to using the laser. (M10/M11 after M3)
Does anyone know what the M3 relay pins and port should be? I dont remember setting them before. It doesn't seem to be working using the default pin0 port 0 values. Do I need to enable the laser output or change PWM pin assignment values? Port 1 is unused on my UC3005LPT. Do I need to refer to these pins?

If you use the M3 only to enable the laser, then the port 0 pin 0 is enough, but you have to set up the laser port and pin.