When I installed the AceSEF component, and enabled it all of a sudden the PDF linksdid not work anymore, it opens a new window but instead of displaying the PDF version it displays the HTML version of the page, when I disabled the AceSEF component it works again.
Luckily I managed to solve this problem. Please see the Answer
Open the AceSEF configuration page and click on the URLs tab.
Under the Global Variables section in the non-SEF variables section, add the following format=pdf, clear the cache refresh the page and the PDF link will work again.
