The default click-once version of Report Builder that will be used with SQL Server 2008 Reporting Services is Report Builder 1.0. If the Custom Report Builder Launch URL was modified to use Report Builder 2.0, then Report Builder may no longer work following an upgrade to SQL Server 2008 R2 Reporting Services. The SQL Server 2008 R2 version installs Report Builder 3.0, but the Custom Report Builder Launch URL is still configured for Report Builder 2.0.
Use SharePoint Central Administration to update the Custom Report Builder Launch URL to an empty string. This will set the property back to the default, which is Report Builder 3.0. For more information, see How to: Configure Report Server Integration in SharePoint Central Administration.