This post is to help anyone who happens to build a network using Pro Sites, and uses Project Wonderful ad code.
I had an issue that I wanted an ad to display in-post and page on the FREE level so I had set the Ads per Page to 1. I had also put an ad in the shared common header, and a small strip of 3 ads in the common footer. So those ads displayed fine, but the in-post one did not show.
After two weeks of discussion and working with help, we hadn't figured it out. But then it struck me, Ads per page...doesn't SEEM like it should be counting the header and footer, but, I changed the number to 5 (one for the header ad, and 3 for the small strip on the bottom...and then 1 for the ad that wasn't showing) and BOOM...the in-post ads appeared.
This is probably a very case-specific thing, but the info needs to be out there in case anyone else ever wants to include Project Wonderful advertising in their pro sites network.