When I use pdftoppm on a slightly transparent grey region the output comes out completely black. It is customer data so I can't post it online, but I can email you directly (email me at email@example.com) if you are looking at the bug. It seems like it may be related to https://bugs.freedesktop.org/show_bug.cgi?id=91415, although that is in pdftocairo.
The problem appears in older versions on Ubuntu and is still there in version 0.4, from archlinux.
It is once again the problem of a lot of CAD programs, s. also bug 59991:
The "slightly transparent grey region" is created with a grid of over 2400(!!!) thin lines with color black.
If You call pdftoppm with -thinlinemode shape or render it with a higher resolution, i.e. -r 300 or better -r 600, You will see that the problem is gone!
*** This bug has been marked as a duplicate of bug 59991 ***
Awesome. Thanks for the help Thomas. We'll start using using `-thinlinemode shape`. What are the drawbacks to using `-thinlinemode shape` for other parts of the PDF? I'm assuming some lines that at normal scale would normally look black would be aliased and made super lighty?
Created attachment 121801 [details]
Short documentation about thinlinemodes
No, Micah. Thin lines should never vanish, at least not when Your render it with at least 72 dpi. I attach the short documentation I wrote when I implemented the thinlinemode's. Or better, look at "PDF with thin grid lines" from bug 37347, and try that PDF with and without thinlinemode option and different resolutions. That PDF was the motivation for my implementation.
That the grey background disappears in the PDF of this bug when You use "-thinlinemode shape" is a bug in the implementation: it doesn't distinguish in this case if it is a stroke or a fill operation, so even in case of a fill operation it draws the line with a shape corresponding to the line width set by the document. But the document doesn't set the line width, so it's 0 and therefore the line is drawn white.
The patch for bug 94152 repairs that.