I use i3-gaps from the Regolith repo - I don’t install anything else from the repo.
Is there a way to view the file operation Obsidian runs to open the PDF? That might help narrow down what is causing the issue.
Edit: I’ve tried setting an event listener breakpoint on click then stepping through the execution but my knowledge of electron/js is virtually nil, so I couldn’t figure out what is the code that is calling the file open operation.