The issue has something to do with Real Chutes. When both mods are active, a huge drag vector is applied to the Nose Cone. Around 300m/sec ascent it causes the entire vessel to flip similar to when CoA rises above CoM. Using Aerodynamic overlay, you can see the drag.
I fixed it by disabling Real Chutes. Smooth sailing without it. No drag vector. I'm on 1.9.1 Hope this helps.