There are a couple of different issues.
Marco is talking about a motor mixing issues relating to motor mixing, the stability patch, and motor torque/lift linearity. The end result of not properly understanding, implementing, or tuning results in an increase in total lift. This tends to cause an increase in altitude after aggressive yawing. I have a theory on this problem and a yaw controller design improvement that I hope will correct this. However, I can't do this until Randy and I fix what we are calling the onion.
The second issue related to the inertial navigation and is cause by the fact we don't rotate the acceleration corrections to the body frame. Randy initially did this but we removed it and kept it in the body frame because of the interactions between the horizontal inertial feedback and the altitude feedback. This was messing up Alt Hold. The solution is to rotate the accelerations to the horizontal body frame. We have known about this problem and the likely solution for a while but there is only so much time in the day.
Leonard