I am using Eclipse Tomcat6 integration to test my webapp. I start and stop my Tomcat instance from the "Servers" view in Eclipse. However, quite often, a running instance of tomcat seems to detach itself from the integration where the "Servers" tab says that its stopped. However, once you try to start it, it says that address is being used. When I open the Task Manager, I can see that eclipse is still running and have to kill it manually before I can use the "Servers" view again.
I haven't been able to figure out a pattern but it happens very often now.
Not sure why this is happening but you could try to kill it from Eclipse's 'Console' view (square red button there) instead of using Server's view stop button.