I’ve recently digged the problem and found that this could be related (kinda randomly) to a bunch of problems and conflicts with other Joomla feature (such as system cache).

In my own projects im using right now SH404SEF as SEF component and i’ve found it’s a really good piece of software, so here is a recap of the fix/patch for the problem.

First of all upgrade SH404 to the latest release by downloading it from JoomlaCode.

Now open custom.sef.php in administrator/components/com_sh404sef/ and search for a line containing:

$shDefaultParams['sh404SEF_PROTECT_AGAINST_DOCUMENT_TYPE_ERROR'] = 0;

and set the paramenter to 1:

$shDefaultParams['sh404SEF_PROTECT_AGAINST_DOCUMENT_TYPE_ERROR'] = 1;

If this line is not present then add it at the end of the file.

Now go to the backend panel in Joomla and purge all SEF url by:
Components -> SH404SEF -> Purge SEF Urls
then clear the cache by:
Tools -> Clean Cache

This will clear all current URLs, so that SH404SEF has to recreate them, anyway your PDF button should work again and the PDF URLs should be as the HTML one with an ending parameter ?format=pdf.

Source: http://extensions.siliana.com/forums/index.php?topic=9509.0

Note: As a side effect you shouldn’t problably be able to use the pdf folder feature to store custom PDFs!