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X axis does not zero on homing and is stuck on (in this case) 180 although it is on 0.
I can´t zero it manually and I have tried restarting both hardware and software.
I did not see this at first because I am not normally on machine coordinates so program stopped when it reached a soft limit
that is 180mm further away, very frustrating.
I could just turn off soft limits but I want to know why this is happening and how I fix it!

The axis homing sets the machine coordinates to the value you setup in the "write offset on homing" parameter of the axis.
Since the homing sets the machine coordinates if you have offset in the current coordinate system then ofcourse the current coordinate system will be offset with that value.

So, for example you have the home coordinate set to 0 and you have a -180 offset for the axis then the current coordinate in that coordinate system will be 180 when homed.

You can set the home coordinate properly and clear the offset for the axis is what you should do.

Never mind, I had the "auto set" box unticked in the axis setup.