I'm using YACReader on my iPad, and having the strangest issue. The speech bubbles and text are just gone from some comics. It almost seems like there are two layers to the PDF, and YACReader is not getting the one that has text on it.

There is definitely text in these comics. If I open them on Dropbox, I can read the text. Just not on YACReader.

I've looked through settings and don't see anything obvious that would cause/fix the issue. How do I fix this?

There is a setting about fast PDF processing. Disable it and reimport the problematic PDFs. YACReader tries to find text in the pages and render them properly while importing but for some reason it failed with your files.

Do you mind send me one of them by email so I can see what is going on?