For custom themes you will also have to make the ad management changes to that theme as well check the mod site for manual install instructions and just apply the theme edits to your theme.
I have checked the manual install instruction at the site and parse installation instructions for SMF 2.0RC2 which is my SMF version and done all the edits (copy/paste etc). Actually, the normal install through Packages worked fine and all the edits were already in place. Therefore, I did not need to change anything, everything was at place.
But, to my agony and surprise, the situation is no different. I tried various google ads also for skyscraper ads etc and yet, no ads are getting properly displayed.
Please help. Also, check the code I had pasted in the above post of mine and point out the errors (if any).