The bug

It appears net.minecraft.server.rcon.thread.GenericThread (Mojang name) respectively its subclasses are not thread-safe:

• GenericThread.running: Is modified outside of thread (stop()), but its value is checked within run(). There are no memory visibility guarantees because running is not volatile.
• GenericThread.stop(): Calls non-thread-safe methods when thread.join times out (might be intended).