Thomas, I had this same issue, realizing my ‘content injected’ ads were not showing, but the others were. I went through all of these messages, and your notes and had no success (with the possible ‘the_content’ issue(s) that may have been in my theme flatthirteen).
Knowing it worked just a few months or so ago, and that I had not added any new plugins that may be interfering, I went back to 1.6.6.1. It worked fine.
So, with nothing changed, except updates to various plugins and core, AND it works with the old version, but not the new version, I’m inclined to think that your code is behaving differently in these newer versions, and that you may still have a bug that subverts the injection.
Thanks for your great plugin.