Automated Scanning, like other Vulnerability Assessment (VA) tools, searches for known vulnerabilities in known products. While it will sometimes find unknown vulnerabilities, this is usually due to similarities to known vulnerability signatures.
beSTORM exhaustively tests the protocol implementation and will find all known, as well as unknown, vulnerabilities that relate to buffer overflow, format string and off-by-one vulnerabilities (currently over 95% of the known security flaws belong to one of those vulnerability types).
Also, Automated Scanning is used by the end-user for scanning their network machines. beSTORM is used by the software vendor itself, to scan the product during development.