Problems with OnMouseUp

Have you checked the docs about OnMouseUp? OnMouseUp only is called if the mouse pointer didn't moved out of the collider or GUI element since the button was pressed. Could it be the problem? I mean: if the object is moving, you probably will loose it.
I personally prefer to use OnMouseOver - at least I've never had any problem with it:

function OnMouseOver(){
  if (Input.GetMouseButtonUp(0)){
    // do your stuff
  }
}

Another problem: I've heard about strange errors with mesh colliders, like objects disappearing when near to frustum planes. The problem seems to be with their bounds being incorrectly generated by Unity - who knows if it could interfere with mouse-to-object relation? Try to use box colliders or whatever just to test this possibility.