A fellow co-worker of mine was the problem that when converting a Word document to Adobe PDF a link to a webpage would become no longer clickable. Well as it turns out when using the File->Print to PDF option all links are removed and only the links that look like www.example.com are then made clickable.
However this is when we came across a second problem. Using the 'Adobe PDF'->'Convert to Adobe PDF', Adobe PDFmaker would then stop responding after Processing Tag Information. The correction for this was quite simply unchecking the option 'Enable accessibility and reflow with tagged PDF' in 'Adobe PDF'->'Change Conversion Settings'.
The document then converted like a charm, links and all.