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I'm seeing a similar issue as well. I have a matrix job that executes a variety of tests per configuration.
I allow multiple executions to occur simultaneously, on a T2Micro instance, which ends up spawning an instance per configuration run (which is as intended).
Out of, say, 10 configuration executions, around 4 or so will end up showing as node offline. Sometimes I can relaunch the slave agent, other times it times out when attempting to connect via SSH (I see similar results if I attempt to connect directly via SSH).
I really like the idea of the EC2 plugin, but not if jobs/nodes are going to hang. The idea is to save money by running nodes only for the amount of time they're needed, but if they hang indefinitely, that could run up the bill quite fast.