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The problem seems to be with the age of some of these transformations. If you look at the PDF file you linked to quite a few of the TF links are 47 seconds old, if this is longer than the TF buffer used to try and resolve the queries this will result in the failure your described.

Are you running a system on two different computers with some TF's being produced on one of them and some on the other one? Since ROS uses the system clock of the computer this time offset could be caused by the two system clocks being out of sync.

This Answers has a good description of how to fix this using the Chony tool.

If you can sync the time of your two computers then hopefully this problem will be fixed.