This ones is such as oddity, I just had to share.
Every time I joined a Windows 8.1 or Server 2012 R2 computer to my domain, and logged on with a domain user account, the Start Screen would reset back to default.
I ruled out synchronization between SkyDrive (OneDrive). If I set the file that contains the Start Screen settings (“%LocalAppData%\Microsoft\Windows\Microsoft\Windows\appsFolder.itemdata-ms“) to read only. The tiles would remain. I did some remote ProcMon digging and could see the system would attempt to right to the file during logon only.
I moved the computer and user into an OU with no applied GPOs, then just the computer and finally just the user. In the end, I nailed it down to a particular OU and its GPO. I turned off all the Policy settings that related to “Start Menu”, no change. I created a new GPO, disabled the old and started to rebuild the settings one-by-one. The problem had gone away. I had several Preferences applied so I copied them from the original GPO. The problem returned. So I had nailed it down to a GPP. Within the GPP were some registry settings controlling Explore, hidden files and Start Menu appearance. (HKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\Advanced).
There were several settings referring to the Start Menu. One in particular caught my eye: StartMenuInit. A quick google returned this page. My GPP was setting this value to 4: “Windows 7 Shell”. This works for Windows 7, but not Windows 8.x.
I disabled the particular GPP entry for StartMenuInit and the problem was solved.
I guess the moral of the story is, do not assume group policies designed for an older OS will work with the newer releases.