First of all, I understand that Aerodynamic forces can cause a rocket to lose control, and also that changes in the center of mass can, but now that I have eliminated those two possibilites I know of, I'm stuck. The rocket I am working on is a probe version using a different upper stage than the original, but the rest is the same. The center of mass in every stage is also almost completely the same.
Of course the probe version didn't work as planned. It will go through it's first booster stage and raise it to around 12k meters. Then that stage is ejected and immediatly afterwards, then the second stage (which is supposed to be stable, it has wings and an okay center of mass) starts flipping around.
Observations -
It seems as if SAS makes it worse, but turning it off dosen't fix the problem
If I start the rocket on it's second stage (It will fly to the same place it flipped at) it dosen't become unstable even though it is at the same inclination and altitude that it would begin it's burn.
I turned off the wing's yaw and roll control on the whole rocket, the same kind of unstability occured to the rocket directly after launch.
I really am unsure of what is causing the unstability, I will answer any questions about it if anyone asks!