Veera,
Can you tell me if you do not restart the Windows machine but instead just restart the SiteScope service will this also temporarily resolve the issue? I know that there were a lot of pefex related issues in the early versions of 9.x and this sounds like one since a restart of the box (and most likely a restart of the sitescope service) will resolve the issue. At this point I do not believe that there is any other permanant solution than to upgrade to a 10.1x or perferrably a 11.2x version of SiteScope.