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This seems to be indeed related to the two referenced issues. I don't know a workaround for this case but it looks like you have already received an answer to your question on answers.ros.org.
I will close this ticket since the question is already covered by answers.ros.org and the referenced issues already track the source of the problem.
My issue, including an exemplary .bag file, are described here:
http://answers.ros.org/question/261187/bug-rosbag-filter-and-tf_static/
I am running Ubuntu 16.04 and ROS kinetic.
This may or may not be related to topic latching, and these issues:
#685
#679
Any quick fix or workaround for the .bag files I already have?
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