Ok, so I have a pretty weird bug going on here. I'm using v0.3.0.0 of BDAc with v1.3 of KSP. Stock aerodynamics.
Debug labels reveal that sometimes the plane thinks it's going to have a collision, so it pulls either straight up, or flips over and dives for the ground. I'm using the combined weapon manager and autopilot antenna that comes in Aviators Arsenal. But I've had this happen with the standard parts too.
If I need to report the bug anywhere else, or you need any more info, do tell and I shall.