Been trying to find a solution and managed to find out what was causing the problem with the heading settings.
The main reason was I didnt fully understand how it all fits together.
I had assumed the header sizes were set by ckeditor so I had deleted the header styles from the main style sheet.
By trial and error I found that ckeditor sizes for h1 was 24pt, h2 was 18pt and h3 was 14pt so added these back in the style sheet and the headers work ok now.
The only problem I have left is how to set the default font size for text inserted in the ckeditor editing window. I've tried changing the font size from small to large in contents.css but it doesnt seem to change the font size as you enter text. The font size can be changed by selecting it and choosing from the size dropdown so that works ok.
If you can point me in the right direction on this, shouldn't need the support ticket.