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I think I'd have to see a bag file and full configuration. Re: this point

The IMU data are all temporarily set to 0 (for debug purposes), and only an irrelevant axis (e.g., Z'') is configured to be active

How is your IMU mounted, and what is the base_link->imu transform? I am also very suspicious of the fact that your IMU Z acceleration has (a) a value of 0 and (b) a massive covariance in the sample message. Covariance values can have subtle effects, even in other axes.

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