Hmm It looks like your CSS is conflicting with the hotspot stuff and pushing the highlighted divs down.

I see that your toolbar looks like it's been tinkered with a bit, I wonder if there's something in your version of the core that is off, or if its theme related. I'd try:

1) Make a new empty page of the current theme and see if its happening there. If not its something you've placed on that specific page that is conflicting with your style.

2) Switch to a clean theme like Greek Yogurt and see if it does it there. If so it's something with the modifications you've made to the core for white labeling.

3) Try using your custom theme on a clean concrete5 core, if it happens there, it something with the CSS for your theme..

Last thought... There's tricks people to do wrap the whole page in a div to push it down if your toolbar exists.. Perhaps one of those is getting called twice.

Thanks for your comments Franz, I'll work through them and let you know how I get on - one thing it won't be is the white labelling - all I've done there is replaced the original image with a new one.

Looking at it, I think it must be something to do with the C5 edit bar, as the distance the hotspot highlighter is pushed down matches.