Hi Jacob,
Are you still seeing this issue? Could students be timing out of Moodle before they save or submit their responses?
We have had students report that their responses were not saved. The instructor suspected that students left their computers before submitting the questionnaire, and then they timed out.
I did some testing. I found that some types of questions, including the essay, do auto-save. Thus, even if Moodle times outs, essay answers remain and can be submitted upon log in. However, other types of questions, such as yes/no and check boxes, do not auto-save. These are lost if the user times out.
If this is your issue, you can resolve it by putting page breaks between questions. When students advance to the next page, responses are saved.
The Quiz activity works the same. It will also look multiple choice type questions if students, unless students have advanced to the next page of the quiz.