In order to check the WSUs server that the clients are contacting and also check for any GPOs affecting those clients, you will need to check the following:

Rsop.msc on the client...
Check the Computer Configuration > Administrative Templates > Windows Components > Windows Update > is it listed the correct WSUs server?
Check also the registry settings under the HKLM\Software\Policies\Microsoft\Windows\WindowsUpdate reg key..

Compare the below registry keys on a "problematic" machine, with the same  registry keys from a “working” machine:
HKEY_LOCAL_MACHINE\Software\Policies\Microsoft\Windows\WindowsUpdate
HKEY_LOCAL_MACHINE\Software\Policies\Microsoft\Windows\WindowsUpdate\AU

- Follow the below TechNet article:
Troubleshooting Group Policy Configuration for Software Updates http://technet.microsoft.com/en-us/library/bb735866.aspx

- Check if WSUs is defined in the GP (i.e: server name and port) versus how it is set in ConfMgr (i.e. FQDN)

- Check the WUAhandler.log for the WSUs URL used.