Some systems may cause external apps to override pdf.js?
A Linux user just showed me an old TBB that they had upgraded since 4.0 to 4.0.4 using the updater, and this TBB had extra entries for PDF in the browser Preferences->Applications window. This caused Tor Browser to try to launch an external application to handle PDFs. The Torbutton external application warning was displayed, and if accepted, a system PDF viewer would be used instead of pdf.js.
When they installed a fresh TBB on the same system in a new directory, it did not have these entries, and used pdf.js.
It's not clear if it was updating that caused this issue, or if something else previously changed TBB on their system while it was running.