System.out.println and System.err.println out of order

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They are different streams and are flushed at different times.

If you put 

System.out.flush();
System.err.flush();

inside your loop, it will work as expected.

To clarify, output streams are cached so all the write goes into this memory buffer. After a period of quiet, they are actually written out.

You write to two buffers, then after a period of inactivity they both are flushed (one after the other).

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