I am just wondering if it is normal to have discoloured (orangey brown) water coming through the house after running my water softener. I have to leave the water run for about 5 minutes to get the water to return to clear again.

I am in a new house so I wouldn't think it is the pipes, but happens every time I run the softener.

Any help would be great

This is not normal, Do you know hoiw to isolate the softner from the house by closing the three handled manifold above the unit, if so do it and then tell us if you see the discolored water ever in the next several days. Then open the valves and allow the system to regenerate, if you get discolored water call for softner repair, it is not a DIY project at this point.

No this is not normal, if it is possible you will have to increase the final rinse and that will take care of your rusty water after regeneration cycles. It would help me if you could tell the brand you have to help you set it up correctly.
Thank you
Mark