I also had stability problem with plane 4.1. This was reported earlier in post 2226 (or 2197) and there GSoC 20 : EKF3 Affinity and Lane Switching (Merged !)
I have had this problem only with tvbs and only with plane 4.1.dev or 4.1.beta. When I came back to 4.0 this is just fine over dozens of flights. Vectored thrust and control surfaces seems to act against each other. The starting point is always a lane switch message.
I have had a look at your log but I do not see same symptoms !!