I seem to have fixed the problems I was having with the Blue skin. Annoying enough after a couple of hours of messing with the CSS thinking “Well it worked before, nothing’s changed, it just won’t work now. I know I’ll fiddle until it does” and getting nowhere, I took another approach and looked at the templates.

I found that I’d included an extra closing DIV tag which was causing the Menu sidebar to be displayed outside of the main display. After removing this, it worked again (yes I called myself a fool too) and then the only problem was to remember the initial formatting of the CSS file.