I just finished setting mine up and I also had some issues with soft limits.
I just chose not to use them.
My zero points are different, so there are many was that you can setup and use a lathe.
I am using radius mode and have rear tool posts. None of my cuts are in X negative. They are all positive. My Z zero is always set at the end of the stock after a facing. Xzero done similarly after a fine turn cut and measure radius to get the center of the stock.
This method seems to work pretty well so far.
I just uploaded a Youtube video if you would like to see it.
http://www.youtube.com/watch?v=6nNCWBqJOPU