Hi Me again!
You wrote:
"the worst we've done is including links in the footers of some themes we've distributed"
So, perhaps you should start with the worst and see if that is it?
I have a feeling that these Client Footer Links used to provide rankings and now don't because of adjustments to the algorithm. I think that rather than view it as a penalty, you may be best to view it as a previous gift that is now gone. I am formulating theories as to why, and I am currently somewhere beyond my original hunch (which was that they look like paid links), and not yet to my actual theory (which is much broader, but I haven't fully formulated, so I will keep to myself for a bit).
Anyway, I have figured out how it would be quite easy for search engines to devalue Client Footer Links, along with the blog networks and paid links they have been taking down, by using some available metrics. So, when my theory comes together, if the search engines are not using it, they will be forced to sometime in the next few years. (Stroking my own genious ego here, I know).