Not sure how you are making your PDF, but if I were to guess, I would think that you were scanning in a document as "formatted text" in some kind of OCR program and then saving it as a PDF. Formatted text puts your text into a table and makes it so that the text is unreadable by screen readers, which is carried over into the PDF. (it basically see's the text as a "graphic" where each table would be considered a different graphic depending on how you set the order of the text/graphic boxes)
To figure it out more, I would have to know how you are making the document.
To figure it out more, I would have to know how you are making the document.