I did a server migration over the weekend SBS 2003 to SBS 2011 everything went fine except some of the machines would do strange things when it came to moving the users shared folders, I noticed the Desktops would redirect fine but the users My Documents would not update the sync center with the new location or they would have both locations and would appear to be syncing both, like i said very strange things yet some of the machines were absolutely fine.
One of the clues that lead me to believe it was a corrupt csc file was by right clicking on one of the folders that did work eg the My Pictures folder it said it was working offline even though it wasn’t, to repair the csc folder you need to do the following.
Start regedit
1) Navigate to HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\Csc\Parameters
2) Right click go to new and then DWORDValue
3) Type FormatDatabase and press enter
4) On the Edit menu, click Modify
5) Type 1 in the Value box and click OK
6) Exit regedit
7) Restart the Computer