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In your Python script, I guess you were using Bag.write. Did you specify the t parameter and set it to the correct time stamp? As far as I know, that's the parameter that controls playback speed.

The system cannot use header.stamp for a simple reason: not every message has a stamp but rosbag needs time information. Also, the C++ rosbag library uses the raw (serialized) message data blobs to store them in the file. There is just no way to access the header without knowing the exact message definition.