I had the same issue, and here's how I solved it:
Adding it via drag and drop from /usr/share/applications using nautilus was always giving me the duplicated unity launcher icons.
I launched the application from a terminal window and used the "Lock to launcher" right click option on its panel icon, which seemed to work as expected once I dropped into the launcher from nautilus.
The problem was the desktop file from /usr/share/applications has some extra features which the drag-and-drop-generated shortcut(located in ~/.local/share/applications) was missing, like "New Window" and "New file" right click menu options, which I didn't want to lose. So I tried to see what's different between them, and the only significant difference I could see was this attribute:
Once I added that to the .desktop file from /usr/share/applications it started working. I then deleted the generated shortcut from ~/.local/share/applications and it seems to work.
I hope this helps you as well.