Ahhhhhh so I have found out what has happened. I checked the motion tab settings and some how all of the clips aspect ratios under the distort parameters are on -2. Setting this to 0 corrects the problem for export.
The edit is quite complex. Anybody tell me how to “batch” change all the clips motion tab distort aspect ratios?
Not sure how I ended up here but hey at least there seems a way out!