The used ellipsoid is only an approximation of the actual shape of the object. You have to choose a reasonable size for it. In your case, you have rather flat objects, which means that your ellipsoid will most likely look something like (x,y,x) where y is much smaller then x. In addition, make sure that you've set the collision modes properly. More information is here: http://www.jpct.net/wiki/index.php?title=Collision_detection

I'm not sure if the ellipsoid collision detection is the best choice for your kind of application and your objects' shapes. Or at least not the only one. Maybe you want to combine it with some ray-polygon checking of some simple distance based logic that you could do on your own.