I have also noticed that Word Count on PDF's is totally inaccurate. I have a EPUB that gives me 434 pages w/ 119k words, and the PDF gives me 539 pages with 8.9k words. I've noticed as a trend it seems to be close with the page counts but word counts are exceptionally less w/ PDF. I don't really consider it to be a big deal as I hate PDF anyway. Just FYI.
Oh, you can't disable the LIT plugin either as a temporary workaround.
