(1) This is difficult to debug without more information. One thing you
could do is display the pose of the robot corresponding to the last
collision in rviz. This tutorial -
http://www.ros.org/wiki/motion_planning_environment/Tutorials/Tutorial%20B
- helps you do that.

(2) Also, using the rviz "select" button, you can click on the markers
and they will give you more information on what is colliding.

(3) Are you moving the base of the robot around? We are working
towards a release that handles motion of the robot base properly - the
current collision environment is not yet fully tested for motion of
the base.