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I've put together a change to increase the logging detail on this:
https://github.com/jenkinsci/ec2-plugin/pull/101
While reading for this I also noticed that in hudson.model.Computer, getIdleStartMilliseconds() returns Long.MIN_VALUE if there are no executors.
If there are executors, then the greatest of the last executed job time and the executor's owning computer's getConnectTime() are returned. The executor's last executed job time is initialized to the executor's creation time.
The Computer's connectTime is initialized to zero, but is set to the current time when proactive launch begins.
So unless a node is actively running a job on an executor, it's reported as having been idle since creation, even if it's busily running init scripts and other setup so the slave agent hasn't connected and created executors yet.
That's why it's being stopped again before it's started properly.
I think the best fix for this will be for EC2Computer to @Override getIdleStartMilliseconds(...) and report a time in the future (i.e. busy) while the node is still starting and hasn't yet connected its slave agent.
Or at least until the init script finishes running, in EC2UnixLauncher.launch(...)
It looks like testing isOffline() should be sufficient for that - if the node is offline, it's clearly not a candidate for idle shutdown.
To be really picky, we could instead have the ComputerLauncher set a flag on the Computer when init scripts have finished and the slave agent has been launched. However, that's the point at which a channel is registered and isOffline becomes false, so there seems little point.