You're correct Lonkero, I was modifying those keys (but did not post that code) but I was also modifying all the other keys at the same time which apparently was causing some issue preventing it from working. Trimming down the code to only modify the User Shell Folders keys now appears to work fine.
You MUST restart though for the change to take affect
Code:
Break On
Dim $SO
$SO=SetOption('Explicit','On')
$SO=SetOption('NoVarsInStrings','On')
Dim $UpdateMD,$ReadMD,$Key,$NewFolder
$NewFolder = 'D:\My Documents'
$Key = 'HKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\User Shell Folders'
$UpdateMD = WriteValue($Key,'Personal',$NewFolder,REG_EXPAND_SZ)
$ReadMD = ReadValue($Key,'Personal')
$UpdateMD = WriteValue($Key,'My Pictures',$ReadMD+'\My Pictures',REG_EXPAND_SZ)
$UpdateMD = WriteValue($Key,'My Music',$ReadMD+'\My Music',REG_EXPAND_SZ)
$UpdateMD = WriteValue($Key,'My Videos',$ReadMD+'\My Videos',REG_EXPAND_SZ)