Hi Jeff,
 
I've been thinking about the issue I raised. Is it possible that the cause of my problem is including two different copies of boost::shared_ptr?

Yes, definitely.
 
Are there any local edits to the copy of boost used by cctbx?

No. (Currently the boost that comes with cctbx is an original snapshot of the boost svn from the end of July.)
 
In short, if I get the same revision as the listed for cctbx_sources/boost/TAG, can I substitute/overwrite the cctbx_sources/boost directory?

Yes, you should be able to substitute any relatively recent version of boost.

Ralf