Six months before the San Jose-Cisco Systems controversy went public, Leon Nix knew the city risked violating its own rules by favoring the networking company's products in its new City Hall. But he feared speaking out, thinking his bosses might come after him. Now it appears he may have been right. On a January morning, Nix, then the project's budget analyst, reluctantly sent an e-mail to his boss pointing out potential problems with the $8 million contract. A week later, he was taken off the project without being told why. Today, as officials wonder where the truth lies in the...