Windows 7 Pin to Start Menu (2)

So I recently ran into a problem when setting up my new laptop. When I pinned my favourite apps to the start menu Windows would append (2) to the end of the file name, trying to rename it prompts that the shortcut already exists.

Here is what I found, the shortcut is already there but hidden in a folder located here:

%appdata%\Microsoft\Internet Explorer\Quick Launch\User Pinned

So either delete the hidden shortcuts in this folder and remake your pinned items in the start menu or make them non-hidden.