If you changed the metadata, you need to restart your Kindle, this refreshes the "library"
Also, Kindle seems to have a problem with metadata in some PDF files. It helps to resave the PDF with other compatibility settings. If you have Adobe Acrobat, you can do this by going into the (translated from my German version) Extended/Advanced menu -> PDF Optimization -> set it to compatibility with Acrobat 5.0 and higher. Don't forget to deselect everything else you see in the window, like picture and font settings, as they could decrease the quality. Then save the PDF. After a Kindle restart, the metadata should be correct.
Note that Kindle (don't know about Kindle 3 yet, but 2 and DX act like this) don't show the metadata-title, but the filename instead. Kindle does read the metadata (as it puts the title on the Info Page of the file) but only displays the filename in your booklist.