This is caused when you set Notepad++ to run as administrator on Windows 7.
Go into your registry as an administrator and search for notepad++.exe. Find the key under HKEY_CLASSES_ROOT that has an entry with the Edit with Notepad++ and delete the whole key. Right click and you should see that you no longer have that option.
Now we re-create it:
Go to:
HKEY_CLASSES_ROOT\*\shell
Create a new key under shell called OpenWithNotepad and create a subkey under that called command.
In the OpenWithNotepad key the default string is what you want the context menu item to be called. I set it to Open with Notepad++.
Create a new string value called icon and set the value to be the full path to notepad++.exe.
Under the command key edit the default string value and change it to "path-to-notepad++.exe" "%1" where path-to-notepad++.exe should be the full path, e.g. C:\Program Files\Notepad++\notepad++.exe.
When you right click this option it should now ask you properly for giving Notepad++ admin access to a file.
You still need to go to the properties for notepad++.exe and set it to run as an administrator.