Document ID not being set in Libraries Ok. I wasn't sure about the etiquette for answering your own question. I will add it as the answer and remove it from the question.
Document ID not being set in Libraries The DocumentId was originally activated before users began adding content. When I activated/deactivated it for this fix, users were already using the system. The site is somewhere around 45 subsites, with an average of 10 lists/libraries on a subsite.