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I had this issue also (this affects all transparency in the pdf and might not latex beamer related), but it seems that it isn't a direct pdfpc bug.
If you are using an Intel graphic card, you can try to change the "AccelMethod"
in X11 from SNA to UXA. You may try something like this to change the driver
options in your X11 config:
I also tried to fix this in pdfpc, but that might be more work. I changed the
Gdk.Pixmap usage to Cairo Contexts (as suggested in the Gdk documentation). This
solved the issue also, but I was not able to convert all Pixmap usage until now
(not enough time).
Thank you for this solution, it worked for me. However, I found a presentation that was working properly, so I assumed that it has something to do with the PDF version.
Unfortunately I don't have any experience with GDK so I can't argue about the second solution :).
It seems that the images generated by beamer (such as bullets) are not properly rendered.
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