Thanks for the quick response. I have checked the source code for the main board index page and the advertisement code is not there, but it does show in all the other SMF pages. I have selected to show all ads in admin so that I can see where they appear and if they are positioned correctly, but nothing on the index page.

I just switched to the default theme, where I believe the ad mod is meant to automatically be installed, and I get the same - ads in the expected places but not in the index. Also not in the personal messages page as well....
To further clarify, the ad code is in index.template.php