Boinc uses preferences from the site on which you've edited them last time. If you've edited them on another server, this server will delete all extra PG venues, unknown to him.
1. Do not edit settings on other server, do this only on PG. If you're crunching other project, you have to contact PG server once to receive them.
2. Do not use global settings, use local copy on each computer (have own disadvantages).