As per a question I posted a couple days ago I have done some testing to try and further diagnose the problem. I have worked out that when you are using chart symbology with polygon features, whilst prevent overlap is ticked, it causes the exported map image to contain duplicated symbols which are not present on the layout view.
I haven't tested this with line features but I have tested it with point features. Point features display correctly both within layout view and on exported map image.
Is this a bug or is this intended? Have others come across this?