The bounding box does scale with scaling but that doesn't really matter, because collisions in jPCT are always ray/sphere/ellipsoid against polygons, not against the bounding box. That means that your ray (cast from the center of the colliding object) has to hit one of the polygons of the other object. Maybe that's not always the case in your application!? You might try to use spherical or ellipsoid collision detection instead, where the colliding object has an actually "size" and isn't a simple ray with no size at all.