I have a map with points on it which the user hovers over to reveal further information.
The problem I have is hard to explain because it only seems to be a problem when
When hosted from your server, the page is rendering in a browser mode other than IE9 Standards Mode.
For example, if it's rendering in IE7 Mode or Quirks Mode, z-index
problems are expected.
Hit F12 to bring up the Developer Tools, and see which it is.
There are many different possibilities as to why this is happening, see:
http://hsivonen.iki.fi/doctype/#ie8modes
If you just want to fix it without working out where the problem is coming from:
<meta http-equiv="X-UA-Compatible" content="IE=edge">