Some servers are having GPO problems and these problems makes SCCM unable to update the WindowsUpdate registry values so I made this Registry file and imported it to all systems having GPO issues.
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\Policies\Microsoft\Windows\WindowsUpdate]
"WUServer"="http://yyour_sccm_sup_server.xxx.xxx.xxx:80"
"WUStatusServer"="http://your_sccm_sup_server.xxx.xxx.xxx:80"
[HKEY_LOCAL_MACHINE\SOFTWARE\Policies\Microsoft\Windows\WindowsUpdate\AU]
"UseWUServer"=dword:00000001
When the file is imported SCCM detects that there are GPO values and then makes his updates making SCCM patch management to start working.