When you install WSUS 3 sp2 on your SBS 2003 r2 or SBS 2008 after you click finish the post install wizard will launch. There are two ways to handle this.
Hit cancel and the update will pick up the prior settings.
Way two — double check the settings
From Karen Christian
I got an error on the console (‘The software update configuration has been modified and no longer meets the recommended configuration.’) after installing SP2 this morning and rebooting on this SBS2K8 server (TTSSERVER). I fixed it by running MMC with Update Services, Options. This server was a Jeff Swing Migration from SBS2K3. Everything appears to be working OK now on this box.
Here’s the process I went through to fix the problem (maybe it will help someone else):
Start, MMC, File, Add/Remove Snap-in, Update Services, Add, OK. Expand Update Services, expand ‘SERVER’, Options, WSUS Server Configuration Wizard, Next, Next, Next, Start Connecting, Next, Next (only English selected here), select All Products, verify selection of Critical Updates, Definition Updates, Security Updates, Service Packs, Update Rollups (all others are unselected), Next, Next, Next, Next, Finish. Close MMC. Open Windows SBS Console and Updates work once again (no error).