Setting JAVA_HOME should not be necessary if you are using one of our platform specific installers. Like you mention, those packages will install a jre directory for the server, agent and shell in the top-level installation directory.
The startup scripts for HQ determine whether or not the jre has been included and will use it if it's available. I'm guessing there may be a problem with the hq-agent.sh script on RHEL 4.
If you want to give us some debugging info, we can look into it to see if there is a problem. It would be helpful if you could edit your hq-agent.sh and add the line 'set -x' right above the AGENTPROPFILE_PROP=.. line. Save the file and rerun the agent startup script without JAVA_HOME set. If you could attach the output from that command it would be really helpful.
Thanks Vince,
-Ryan