Hi !
I may have a related issue, in position mode with Vision as height source (in a fork of 1.16.0).
The EKF estimated altitude was stable, but the drone was clearly climbing or falling (ev_odometry was consistent with reality but EKF estimated that altitude was stable).
In my case, I believe it is a configuration issue, but I don’t know for sure and the symptoms seem to be close to yours (data are consistent but the EKF estimation is not).