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How is this different in MySQL 5.1?

From the article I get the impression that this is a new problem introduced with 5.5.

It's not. The adaptive flushing algorithm has improved over the various versions, but checkpointing has been the cause of performance stalls for a long time. Here is an early bug report of the problem from 2006.

http://bugs.mysql.com/bug.php?id=19673

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