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rosbag connects to publishers like any other node: http://wiki.ros.org/ROS/Technical%20Overview#Establishing_a_topic_connection
No message sent before the connection is established will be buffered or queued in any way. (For the rosbag subscriber, other subscribers with established connections will queue as expected.) Anything sent during the negotiations will be dropped.
As @ahendrix mentions you should make sure to use the embedded timestamps not the time or receipt. And if those are off I would suggest looking at your data sources to make sure that they are applying timestamps correctly and their timesources are synchronized.
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