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I can confirm this reproduces for me as well on 2.0.2.
Safari Version 10.0 (12602.1.50.0.10) on MacOS Sierra 10.12.
The thumbnails for PDFs show up fine in Google Chrome Version 57.0.2987.133 (64-bit) on the same machine.
Noteworthy perhaps that folders that contain nothing but PDFs still get a thumbnail (this is of course without having a folder.jpg), so something is generating fine for that case but not the other. You can then drill down into the folder and none of the PDFs theselves have a thumbnail.
Has anyone tried this theme out with the new Ubooquity 2.0 yet?
not a developer, but couldn't you just assume a folder.jpg file in the same folder as the files?
Added 2dcloud, Bergen Street Comics Press, Man of Action Studios, Rizzoli/Universe, Bloomsbury Publishing, Hill & Wang, Atomeka Press, and SelfMadeHero. I think I'm pretty much done for now..!
Added CrossGen. Coming to a close here, only a few more on my plate, unless someone else wants one..!
oh, and Apparat.
Added King Hell Press and America's Best Comics
Just added Stranger Comics, Dreamwave Productions, and Knockabout.
Customer support service by UserEcho

I'm not using reverse proxy FWIW.