Recently, one of my users has been reporting that a small number of the PDFs they are uploading to their site have been generating negative thumbnail images. The PDF itself looks fine when opened, its just the thumbnail. Its only happening to about 5% of the files they upload. This is an example: http://pennds.org/archaeobib/items/show/36814
I can’t confirm the issue with Omeka 2.7.1. The only relevant changes I can think about for this kind of issue happened many versions ago, though. Other than a fairly old version of Omeka itself, the only things I can think of would be problematic versions of ImageMagick or Ghostscript, though I haven’t seen this specific behavior from that kind of problem, to my knowledge.
I’ll note that I couldn’t reproduce your problem with the specific PDF you linked to, so it’s possible that simply upgrading Ghostscript resolves this specific problem, as that’s the most significant difference in the relevant programs here between you and me.
I reached out to our hosting provider and they can’t update Ghostscript atm, but I’ve been mostly able to work around it by having the user “Print to PDF” the PDF (yes, I know it sounds silly, but it seems like the easiest way to reset whatever properties of the PDF are causing the problem). If the hosting updates Ghostscript anytime soon, I can post here if it works. Thanks so much for having a go at it.