I think you are in the wrong space, one is for the old style quick launch while the other is the start menu programs group.
Your personal setup
C:\Users\Your Login Here\AppData\Roaming\Microsoft\Windows\Start Menu
The place ALL users see programs from
Try placing things into that location.
Also pinned refers to things on the bar it self not within the menu you get from clicking and all things should be under the All Programs group while most used things will make it to the other list you post an image of.
You can FORCE something into that list by pinning for sure. just right click what you want and select "Pin to Start Menu" from within the all programs section or even by start searching for it.
Right. I went through the painful process of taking all the shortcuts out of "C:\Users\Jacob\AppData\Roaming\Microsoft\Internet Explorer\Quick Launch\User Pinned\StartMenu"and right clicking to add them to the start menu. I then deleted the original shortcuts and removed the (2) at the end of the shortcuts. Thanks!