Not sure if it's the same issue, but I installed AdSense Manager and everything was working great at first. I put 2 ad units in my sidebar and all good. Then I started putting ads within the posts, which also worked great.
However, the ads stopped appearing in my site's homepage.
I searched everywhere and couldn't find an answer, to the point that I came close to just deleting the plugin. Until I realized that Google's terms or usage allow only 3 ads to be displayed in one page and the AdSense Manager plugin honors this. If you have more than 3 ads in a page, only 3 will appear, the other ones will just not show.
In my homepage, I had 2 units in the sidebar and each post had at least one. I changed the homepage to show excerpts of the posts only with no ads and the sidebar ones reappeared.
Hopefully that helps.