Hi motopsycho, and welcome to PhpDig.net!
It sounds like just the page with the links is getting indexed but not the PDF files. First make sure that the config file is set to index PDFs. Next, if you have access to shell, see if you can call the binary on a PDF. Also make sure that the directories to the binary and the binary itself are set to 755 permissions. Last, if you are using PHP 4.2.2/3, either upgrade or try the mod in
this thread. Once the PDFs get indexed, you can delete the page with links from the admin panel so that it doesn't appear in the search results.