So I have a very thin cube and I've put it in my environment, I've told this cube to let people pass through it using logic bricks. I'm using it to count your score, but when I pass through it I spin randomly out of control. If it helps you have to be in the air to pass through it.
First, make sure that "Ghost" is checked and "obstacle" and "collision bounds" are unchecked in physics. Check that the base and top face are far enough up apart on the Z axis so they do not collide with the avatar. You may want to change the cube into a plane to prevent this from becoming a problem. It would help to know what version of blender, it may be a bug, and what your logic bricks look like.