Why do I appear to have rocks with total kinetic energy higher than the barrier capacity that are not passing through the barrier?

The barriers in RocFall only consider translational kinetic energy for the capacity of the barrier.  The ETAG 027 standard that is used by Geobrugge to test RocFall barriers does not consider rotational velocity as it uses a straight vertical drop of a boulder for testing.

If the translational energy is below the barrier capacity, and the barrier is set as completely inelastic, the rocks hit the barrier, stop entirely, and fall to the ground.  For rocks that are over the barrier capacity, RocFall decreases their translational energy by the barrier capacity.

The effect rotational velocity would have on a barrier is quite complex to model in a meaningful way and is outside the scope of what RocFall is designed for.