Web.config
Server.config
SOAP interface
Check binding elements in AssertServer’s web.config
Publisher
Validation
Validate operation, i.e. when issue a Validate on the whole database, uses the PublisherCommandTimeout setting for SOAP send/receive timeout. It will override the binding defined in AssertServer web.config.
Database queries uses same parameter, PublisherCommandTimeout, for database access in SqlServer.
Also check the log file for duration figures, to get an estimate on what a sufficient timeout may be.