This unfortunately is a common problem in the Windows Security Center and can be a bit of a pig to resolve. Did you reboot after the deletion of the wbem\repository sub folder ?
You said earlier you tried everything so I have little to go on as I might simply be repeating something you tried. If none of the suggestions below don't work then you are probably left with changing the WSC settings 'Change the way Security Center alerts me' uncheck the anti-virus option. Whilst this isn't satisfactory it is likely to be the only way not to get constantly nagged.
WSC doesn't detect avast! -
http://www.microsoft.com/technet/scriptcenter/topics/help/wmi.mspx#EQKACDid you try this:
Windows XP SP2
Start, Run, type cmd and click OK from the command prompt type 'rundll32 wbemupgd, RepairWMISetup' without the quotes and enter.
Or
rundll32 wbemupgd, UpgradeRepository
Note: that the above parameters RepairWMISetup and UpgradeRepository are case-sensitive and must be typed exactly as shown):
Have (or did) you another AV installed in this system, if so what was it and how did you get rid of it ?