The problem is a classic management bureaucracy coupled with an environment changing at the pace of Internet time. To borrow from the Cluetrain Manifesto, the Patent Bureaucracy has built a wall around the examiners, keeping the patent database controlled and the examiners without the means to communicate with their marketplace of inventors and inventions. The system for the distribution of patent information is not transparent and not efficient. It does not work and the result is bad patents and a lack of clarity in the definition of intellectual property. Look at the question of obvious patents.
Corporations filing a patent have no incentive to do a search of the prior art.
To do so would only uncover inconvenient facts. Patent examiners have bad tools at their disposal and operate inside of a closed system. They do searches, but do not have the tools at their disposal to systematically find prior art relating to a proposed patent. They operate behind a wall. We can't see in, they can't see out.