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Can you post a bag file? The problem with not having a velocity reference is that those accelerations are going to compound, so even if your acceleration is only slightly biased, it's going to take off pretty quickly. Double integration is really ugly. I imagine this will be exacerbated by the rapid growth of the covariance matrix for the variables that aren't directly measured.

This won't help, but just as an FYI, you should probably fill out the covariance matrices for the angular velocity and linear acceleration.