This is very bizarre. I have imported an old project to work on. Everything seemed fine until I wanted to adjust the panning on two channels. I suddenly noticed that when I panned the channel/track left the stereo output showed it being panned right. I soon discovered that this was the same with all mixer channel and arrange page adjustments. It seems to only affect this project. I have temporarily solved the issue by changing the Stereo out to fit the issue. (Made L>R and R>L in Combined Panner which turns the Combined Panner orange).
Now I can accept that I have done something wrong, but I am damned if I know what I have done.