Update: I have a dev sandbox running on my laptop and just confirmed the same behavior happens there as well.
So if the file's actual creation time is 15:00 for example (in the metadata of the file itself), it shows up as 22:00.
I started to dig around and when I use a text editor to view a sample PDF file, I can see that the UTC value is in the PDF metadata itself:
The 2159 there is 21:59, when the date created shown everywhere else (Adobe Reader, on the file server, etc.) shows 14:59. And I just created this PDF myself, so I know I actually created it at 14:59 local time.
This leads me to believe that the standard for PDF is for this piece of metadata to be converted to UTC upon file save.
WP-Filebase is *likely* pulling file_date from this metadata field for PDF files, since the dates I'm seeing in Filebase are all UTC.
Perhaps for PDF files, WP-Filebase should be pulling file_date from another field in the metadata?