I just gave this a try on my local setup. Going by your logs, it appears that 
you have placed beans.jar in the deploy folder and the beans.jar contains EJB2 
beans. I used a similar application named myapp_ejb2.jar and placed it in 
deploy folder. Started JBoss. Here's what i see on the console:

  | 20:39:39,739 INFO  [EjbModule] Deploying HelloWorldBean
  | 20:39:39,989 INFO  [ProxyFactory] Bound EJB Home 'HelloWorldBean' to jndi 
'HelloWorld'
  | 20:39:39,989 INFO  [EJBDeployer] Deployed: 
file:/D:/JBoss-4.2.2/jboss-4.2.2.GA/server/jaikiran/deploy/myapp_ejb2.jar/
Then i 'touched' the ejb-jar.xml to redeploy this application. Here's the logs 
that i see:

  | 20:40:05,646 INFO  [EJBDeployer] Undeploying: 
file:/D:/JBoss-4.2.2/jboss-4.2.2.GA/server/jaikiran/deploy/myapp_ejb2.jar/
  | 20:40:05,661 INFO  [ProxyFactory] Unbind EJB Home 'HelloWorldBean' from 
jndi 'HelloWorld'
  | 20:40:05,661 INFO  [EjbModule] Undeployed HelloWorldBean
  | 20:40:05,849 INFO  [EjbModule] Deploying HelloWorldBean
  | 20:40:06,021 INFO  [ProxyFactory] Bound EJB Home 'HelloWorldBean' to jndi 
'HelloWorld'
  | 20:40:06,021 INFO  [EJBDeployer] Deployed: 
file:/D:/JBoss-4.2.2/jboss-4.2.2.GA/server/jaikiran/deploy/myapp_ejb2.jar/

Looks fine for me. Can you search for the string  [EJBDeployer] Deployed: in 
your server.log? 

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