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It's likely that you're starving your listener of time to subscribe and receive incoming messages as you're continuously calling lookup_transform and never letting the node process incoming messages. If they are coming in enough you definitely won't get them all in the first pass while the buffer is filling and you need to make it robust to retrying the queries after the connections have been established to the different sources of the tf streams.

Take a look at the tutorials where there's a try/except block and a sleep.

http://wiki.ros.org/tf2/Tutorials/Writing%20a%20tf2%20listener%20%28Python%29