First : which version of Jahia did you use ?
In case of 4.0.6 ... You must to apply 4.0.6_01 patch or read http://www.jahia.net/jahia/page611.html to correct a problem in "Office documents" indexing (loss tm-extractors-0.4.jar library). This patch is not enough to correct the index of PDF documents.
Perhaps your PDF are password protected. In this case the only way is to remove the password protection...
If your PDFs are not protected, try to reindex all your site by using the site administration wizards.
Becare full of the time to do all the indexing operation because the index are first deleted. So if your session is to short to terminate the indexing the index will be empty. In this case, you must increase the session timeout... (in tomcat conf files).
