WSUS issue: directory permissions and shares disappeared

CURRENT CONFIGURATION: Windows 2003 R2 x64 SP2, WSUS 3.0 SP1 and remote MS SQL 2005 server
OBJECTIVE: Fix issue with WSUS directory permissions and shares.
ISSUE: WSUS folder content was restored to the same location D:\WSUS but with folder and share permissions issue. WSUS shares were disappeared after server restart. 
Server Event ID: 10012 The permissions on directory D:\ are incorrect. 
Clients logs:
80070005    AutomaticUpdates    Failure    Content Download    Error: Download failed.
Use \Program Files\Update Services\Tools\wsusutil.exe
Create new empty folder WSUS2
Run next commands.
"C:\Program Files\Update Services\Tools\wsusutil.exe" movecontent D:\WSUS2 d:\move.log -skipcopy
"C:\Program Files\Update Services\Tools\wsusutil.exe" movecontent D:\WSUS d:\move2.log -skipcopy
It would takes a while.
Successfully stopped WsusService.
Beginning content file location change to D:\WSUS
Did not copy files due to -skipcopy flag.
Successfully changed WUS configuration.
Successfully changed IIS virtual directory path.
Successfully removed existing local content network shares.
Successfully created local content network shares.
Successfully changed registry value for content store directory.
Successfully changed content file location.
Successfully started WsusService.
Content integrity check and repair...
Initiated content integrity check and repair.
Check WSUS status
"C:\Program Files\Update Services\Tools\wsusutil.exe" checkhealth
Done. Please check event log for events with source "Windows Server Update Services".