Four years(!) on and I appear to have exactly the same problem. Same OS (Win7 Pro 64 bit), same context links (7-Zip and Notepad++), latest versions.
The problem seems to be confined to shortcut links. And as mentioned by Antman, only when viewed from certain locations. For instance, all shortcuts within the Documents library (some kind of symbolic link) show this problem. However, navigating to the real location of these shortcuts and examining the context menu is OK.
ShellExView (link above) does not appear to show anything unusual as far as I can tell.
In fact, the duplicate context links are different. The first one refers to the destination of the shortcut (as you would expect), however, the second context menu entry refers to the shortcut (file) itself!! If I pick the second "Edit with Notepad++" menu item on a shortcut that links to a simple text file then I end up editing the binary shortcut file and not the destination text file!