From many hours of research, it appears that CP is not using the correct CPID for reporting stats. All other BOINC projects have updated their software to report stats with the same CPID (I believe that they are all using the external CPID without the hash of the email address.

Other than that, I am quite happy running several BOINC projects so that any occaisional problems with one or more projects does not affect the usability of the extra CPU cycles.