panic - 7:27 pm on Feb 19, 2004 (gmt 0)

I just realized that since it's listing those URLs with the index content, Ink might be treating them as multiple copies of my index, which could have created a penalty for duplicate content. Does this sound possible?

Sounds very possible. The purpose of the multiple content editorial action is to not only stop people from stealing content off of external sites, but to stop people from using the same content and optimizing it differently on multiple pages.