PDF Loading Warner was released as a way to keep jailbreakers secure from the PDF flaw that exists in iOS. While Apple are taking their sweet time to provide users with an update ( probably trying to jailbreak/unlock proof the next update more than focusing on actual user security ), PDF Loading Warner was made available via Cydia to provide an extra layer of security. Everytime you load up a PDF file, PDF Loading Warner asks you for confirmation. Kind of like UAC in Windows.
Since the Clock and iBooks apps also use PDF formats, users got a pop up everytime they used them. This update fixes that annoyance.
PDF Loading Warner is free and very useful. Get it now from Cydia.
You can jailbreak your iPhone and get this security fix by reading this guide on how to use JailbreakMe.