Configuration is :

Master Jenkins on Linux (launched with -Dhudson.util.ProcessTreeKiller.disable=true)
Slaves Jenkins agents on Linux, started by java -jar slave.jar

On Slave agents we have Maven 2/3 jobs where bash script is embedded to start/stop/patch Tomcat applications.
To avoid detached (forked) tomcat to be destroyed, we used the BUILD_ID trick on the bash script.

After upgrading from 1.397 to 1.403, we notice that jobs on slaves where killed.
Same jobs started on Master Jenkins didn't have this auto-kill problem.
Free style jobs on Master or Slave didn't see the problem, so the BUILD_ID still worked.

To restore the correct behaviour, we add -Dhudson.util.ProcessTreeKiller.disable=true on start command line ie :

java -jar slave.jar -Dhudson.util.ProcessTreeKiller.disable=true

I suspect a problem in env vars propagation between Maven 2 or 3 and Jenkins somewhere between 1.397 and 1.403 since now the BUILD_ID env var set by the bash script called by Maven isn't seen by Hudson.