Well... what does your rocket look like? That should give us something to start with. Problems I can think of:
If MechJeb is in control during launch, that could be the problem; it doesn't know how FAR's controls work, so what ends up happening is it tends to over-control and over-correct the rocket.
There's also the possibility that you're just asking for an absurd amount of force to be applied to the rocket to correct its trajectory; if you're flying at full thrust low in the atmosphere when you do this then FAR's aerodynamics will probably apply forces that would tear the rocket apart in a real scenario.
Another possibility is that you're connecting a very heavy part (say a fuel tank) to a very light part (say, a decoupler) that happens to be right near the center of mass of the rocket; such joints are naturally more flexible due to the way physics works in-game and if you manage to get control inputs strong enough to flex the rocket that will ensure that the maximum amount of flexing occurs due to the large amounts of mass on either side of the joint.