Make sure that you have proper write-permissions in the C:\Program Files\Notepad++\ and C:\Program Files\Notepad++\functionList\ directories. You might have to run the installer in Run as Administrator mode to get Windows to give you those permissions, or use Windows Explorer’s right click Properties > Security > Edit (or Advanced) to give your normal user permission on those directories.
Also, make sure that when you run the installer, you don’t have another instance of Notepad++ running, and that no other application has c.xml open. (To make sure this is true, you may want to reboot before running the installer.)