SCCM 4.00.6487.2000 on server 2008 R2 WSUS 3.1.6001.65 on server 2003 with SP2 Looking at Client Installation Menthods, under the software update point client installation published version is blank. The available version is 4.00.6487.2000

under the software update point client installation published version is blank. this means that the client software has not been published to the SUP. So, have you installed the SUP role on your WSUS server http://technet.microsoft.com/en-us/library/bb632674.aspx ??? Also have you respected all steps here http://technet.microsoft.com/en-us/library/bb633194.aspx ? And no chance to use WSUS 3.0 SP2 ;) !!!