I'm guession you use "Run As > Run On Server" to start JBoss ?
This actually not only start jboss if it is not already running it also opens the relavant web sit.
If you do not want that to happen then just Start the server from the server view and deploy the app if needed by Add/Remove action on the server (or just drag'n'drop)
Of course if the app is already there you just need to start the server and everything should be fine.