I've never seen that one. There are some things Acrobat does routinely but doesn't tell you about unless they take a long time. I would try disabling javascript in case document-level or application-level code is doing something (javascript can present those progress bars). If that doesn't stop it, I would suspect it to be an Acrobat function that takes a long time on that PDF (unless it happens with all PDFs).
It also does "retrieving traps" and "trap zones". It's not noticeable on small files, but when I generate 5,000 to 10,000 page pdfs, it really slows down.