Your comments

Right, I do recall thinking the timer wouldn't be great, but I tested a few different things at the moment and just pasted it all. I think the visibilitychange has been the most effective anyways.

I looked into this further and it calls jbig2-imageio to process any PDFs that are/have jbig2 format within them. I am not sure what changed between the versions, but I was able to get it to work by running Ubooquity with 'java -cp Ubooquity.jar:jbig2-imageio-3.0.4.jar com.ubooquity.Launcher --headless --remoteadmin'.
Maybe either the rewrite to kotlin or the pdfbox upgrade? Idk, just sharing what I have.