Go the server Resource's Inventory>Connection tab and see if there is a yellow or red box at the top with an error message that describes why the JON Agent is failing to connect to the managed server. If not, see if there are any error messages in the Agent log (AGENT_HOME_DIR/logs/agent.log) on the machine where the server that is red is running.
A few questions for you -
1) What version of JON are you running?
2) What type of server is the one that is down? - JBoss AS, Tomcat, Apache?
3) If it's JBoss AS or Tomcat, does the remote JMX interface require authentication?