This is indeed really weird. I can’t help you with the rotation matrix.
It seems like your EKF don’t care about the Baro, have you tried modifying the parameters of the EKF ? Maybe the wheight of the Baro ( EKF_ALT_NOISE) is too low or the accelerometer ( EKF_ACC_PNOISE) too high for some reason.
Also your NKF2.AZbias is increasing only on EKF1 and not EKF2. I don’t know what that means because it is also increasing on my copter. But I’ve found several other posts similar to yours while looking for a AZbias problem ( 1, 2, old ).
Sorry, I can’t help you much further than that.