I had the same problem with a Word document and figured out the problem. Word seems to be spitting out separate PDF documents based on the page setup. So under File -> Page Setup you get a dialog box with the settings for the page, and usually a "Format for" dropdown and a "Paper Size" option. If these setting are not the same for the whole document, Word throws a wobbley and generates a PDF for each page setup.
My solution (works where all of the pages are the same format).
File -> Page Setup
Settings: Choose "Microsoft Word" from the dropdown box
Apply Page Setup settings to: Entire Document.
This will setup up the entire document to use the same page settings, and will fix the problem for those of us who are wanting a document that all has the same page settings. (This won't work if you are mixing page sizes.)