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Yea, I added an "echo $JAVA_HOME" shell build step to verify. When running the job, this is what I see in the logs which confirms my fears:
Building remotely on build03 in workspace /data/tomcat/jenkins/workspace/Build-master
Unpacking http://macallan/sources/java/jdk-6u43-linux-x64.tar.gz to /data/tomcat/jenkins/tools/hudson.model.JDK/JDK_6u39 on build03
...
[Build-master] $ /bin/sh -xe /data/tomcat/jenkins/tmp/hudson2047019797614409905.sh
+ echo /usr/java/default
/usr/java/default
The "/usr/java/default" being the default value for $JAVA_HOME on the OS. So even though it's retrieving the correct JDK and extracting it, it's not setting JAVA_HOME to it.
The kicker is that if we don't have a default JAVA_HOME set on the host OS, then the "Default" JDK in Jenkins also never has a JAVA_HOME.