I actually fixed this one myself
In Windows 8 and Server 2012 and above, they use the hidden root folder C:\PROGRAMDATA. To be 100% sure on your system type SET ALL from a command prompt; this will display the value for the ALLUSERSPROFILE system variable and will tell you the path.
So for me, all I needed to do to fix the issue was to create the STARTUP folder in the following path:C:\ProgramData\Microsoft\Windows\Start Menu\Programs