Microsoft has just updated KB Article 2874780:
The Service Manager connector to Configuration Manager does not transfer uninstalled software information
Summary:
Software that is installed on computers is successfully brought over to Microsoft System Center 2012 Service Manager through the Configuration Manager connector. However, when you uninstall the software from a computer and then perform a hardware inventory in System Center 2012 Configuration Manager Service Pack 1 (SP1), the software-installed relationship is not removed in Service Manager even though the relationship is successfully removed in Configuration Manager.
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