I have wordpress 3.3.1 with multisites enabled and working with two blogs - the main and one sub blog.
It works fine on main blog but on secondary blog it does not work on the blog page or other pages. Works fine on single post page and category page.
At first I thought it was because my the blog on the second site is the home page but I checked on the main site (because I currently have a static page as home on main) and it worked fine there as the blog posts as home.
All my settings are exactly the same on each blog as far as the author advertising setup goes. You can see the place holders where they should be but no ads where ads are working fine elsewhere.