Hi Stuart,
It's hard to help when I can't see the exact problem, but from your description, I would suggest looking at the element stacking.
If you have set Absolute properties, you may have caused this ad to force itself over another element. Try using relative positioning options in your CSS.
Without seeing the code & the site, I can't be any more specific. There are lots of tutorials on CSS and Coffeecup have an introductory guide which covers CSS3 here:
http://www.coffeecup.com/books/intro-to-html5-and-css3/.
There's also a comprehensive help file included with Coffeecup StyleSheet Maker which can get you going in understanding how all the elements work and how to use them. Download the trial version here if you don't already own the registered version, the help file is included with both:
http://www.coffeecup.com/stylesheet-maker/
Best of luck with it.
Dave
PS, you could publish the problematic code and site to
www.yourdomain.com/test or any temporary folder, then we can look at it and figure it out with you while your live site would remain as is.