Thanks Wacov, your suggestion has helped me resolve my problem. My earlier post is incorrect, setting ballast blocks to the 'ignore' state does eliminate them from the mass of the overall group, so the joints do go flexi. However using the overall group shape as default seems to get around the unwanted collisions provided any colliding sub-groups are set to 'ignore'. I can now place my ballast anywhere because although the overall group can be huge its not getting used in collision calculations.
Another property of note is that the largest ballast needs to be concealed within the connected group, NOT the group containing the joint itself.
Many thanks, I don't think I would have worked that out, definately not in the short term anyway.