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If synchronization between different contributing machines is off, this can generally cause a lot of problems with tf. The recommendation is to use chrony (http://chrony.tuxfamily.org/) instead of plain ntp for synchronization, as it is much more reliable.

There are quite a few posts on the mailing list about details: http://ros-users.122217.n3.nabble.com/template/NamlServlet.jtp?macro=search_page&node=122217&query=chrony