Ok, figured this issue out. However, I am not real wild about this problem happening during the 8.1 upgrade process.
The problem was missing shortcut entries in:
c:\User<user>\AppData\Local\Microsoft\Windows\WinX\Group1
c:\User<user>\AppData\Local\Microsoft\Windows\WinX\Group2
c:\User<user>\AppData\Local\Microsoft\Windows\WinX\Group3
I copied the entries from the non-administrator account I had created, rebooted, and everything is as expected, including windows + x.
I have experienced exactly the same problem with my work PC on a domain. When you log in with any admin account that has local admin rights on the windows 8.1 it fails to put the winX folder in place all non admin accounts get this folder. Copying this folder
solves the problem immediately no reboot required. A big thanks for solving this as I upgraded as soon as 8.1 came out and googling this problem came up with nothing! It has been a constant irritation since then. sorted! :-)