Hi David,
This typically happens when your PDFs are full of content people want. I have seen this personally with a previous company I worked with and their spec sheets (it was for a software copy). This is good and bad - good people find your content awesome and are linking to it - bad that your PDFs are ranking vs your pages.
Solution - make your pages better. You could potentially take the content from your PDFs and make a page - this in theory should still compel people to link to you. If your PDFs are massive in size, you could consider condense the contents into a webpage that contains FAQs, a summary of the information, etc.
This isn't a bad problem to have. If you can't beat them, join them - optimize your PDFs for search.
Hope this helps.
Mike