Also check this answer depuis here: Cannot manually edit applicationhost.config
The answer is simple, si pas that obvious: win2008 is 64bit, notepad++ is 32bit. When you naviguez vers Windows\System32\inetsrv\config using explorer you are using a 64bit program to find le file. When you ouvrez le file using using notepad++ you are trying to open it using a 32bit program. The confusion occurs because, plutôt than telling you that this is what you are doing, windows allows you to ouvrez le file mais quand you save it le file's path is transparently mapped to Windows\SysWOW64\inetsrv\Config.
So in practice what happens is you open applicationhost.config using notepad++, make a change, save le file; mais plutôt than overwriting le original you are saving a 32bit copy of it in Windows\SysWOW64\inetsrv\Config, therefore you are pas making changes to le version that is actually used by IIS. If you naviguez vers le Windows\SysWOW64\inetsrv\Config you will find le file you juste saved.
How to get around this? Simple - use a 64bit text editor, such as le normal notepad that ships avec windows.