Ok, I managed to properly pin it to the task bar and the icon doesnt duplicate.
But I still can't pin something to the start menu.
It's weird because if I right-click on the program to pin to start.. it says it's pinned, and even shows *NEW* on the apps menu. But when you go in to the apps menu and scroll down its not there.
I also tried editing the shortcut that the 32bit version firefox used in the start menu. But when I changed the properties, the file path and target, it says it can't do it when I click apply. It won't even let me create a new shortcut in that shortcut menu area.
I'm wondering if there is a menu somewhere that deals with the shortcuts in the start menu somewhere.
Edit:
Ok I did a SFC /SCANNOW command to check for any errors. It didn't find any. But I noticed that the pin to start doesnt even pretend to work now.
So I tried again to modify the current Mozilla Firefox shortcut. This time instead of saying I couldn't do it, it asked me to continue as administrator. So I clicked apply and changed the shortcut location. So it now points to the 64bit version of Firefox.
So I guess my issue with firefox is fixed. I do find it odd though that there seemed to so much problems with me installing this 64bit version. It didn't setup any of the new shortcuts for me, yet I know it has for other people. I guess there is a bug somewhere in there. I've noticed other people have similar issues and even after a re-install they still eventually run in to it.