Would it be possible to get a sample project showing the problem?
Is this using the CC sample code or all your own systems? ApplyImpulse ultimately just changes PhysicsVelocity anyway. What direction is the impulse being applied? Can you draw it on screen to help with diagnosis (or point out the impulse)?
Are there issues with local/global reference frame (e.g. are you applying the impulse in local space when the ApplyImpulse function is expecting world space)? If the impulse is pushing the CC into the floor, leading to an interpenetration, then you will get an upward impulse pushing the body out of the floor.