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Problems solved.
In short, the PLICP algorithm in laser_scan_matcher is deterministic, while the whole package's I/O are not due to ROS topic communication.
Anyone interested in this may check with modifying the package:
1. Disable subscribers
2. Read your rosbag using C++ API
3. Directly write the result into a file
Then you can see the results are identical everytime.
Thus we can conclude that the differences are from ROS topic communication. My observation 1 may just be a coincidence.
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