To deactivate the Apache Tomcat configuration tool, that is responsible for the Alert message: "An Instance of Tomcat 6 is already running" is possible by deleting the specific Windows Registry Key.
See WebOffice10R3-DVD\Software\Miscellaneous\tomct6w_autostart_reg_key.reg (64Bit Tomcat) respectively WebOffice10R3-DVD\Software\Miscellaneous\tomct6w_autostart_syswow6432_reg_key.reg (32Bit Tomcat) for the registry key to delete.