We publish almost all of our PDFs to SharePoint. (I'm not certain what version we are using, though.) Users who retrieve these files and click a submit button do not have a problem with submitting as PDFs.
Are the users accessing the form from SharePoint clicking the same submit button? If they are not hitting the same button, can you verify that there is no difference in the code?
If they are using the same button, can you verify that the script to submit the PDF is the same? For example:
This sends the email in a different format depending on which radio button is selected. I'm wondering if there's a select or condition statement that looks for something to be filled in on the "second part" that may be changing how the item is submitted.