I don't know all the ins and out of it, but here's my fast and dirty explanation.
Prior to the events of September 11th, cockpit jumpseat access for 121 flight crew members was pretty much permitted, within the limitations of company policy and the individual crews. A pilot crew member for carrier A was permitted to occupy the cockpit jumpseat in carrier B's plane, having a valid company ID (and in some cases, valid pilot certificates) would get you in. After September 11th, in the resulting shakedown of security procedures, an individual's eligibility to access the cockpit jumpseat, and the verification of said eligibility was called into question. So, access was permitted only if your status could be verified. Initially, the only way to do this was by verifying your employment via the company's computer system (at least in the case of my carrier at that time). Since carrier A's system was not tied into carrier B's system, if a pilot from A wanted to jumpseat on carrier B, he was not granted access to the cockpit, and could only sit in the passenger cabin.
By not allowing access to the often only remaining seat on the airplane, this created a bind for many pilots who relied on that priviledge to commute to and from work. Hence the CASS system was started. As far as I understand, it is a nationwide database that allows participating carriers to verify the eligibility of a crew member requesting cockpit jumpseat access. If the agent boarding the flight can verify your status as a legitimate 121 flight crew member via the CASS system, you can occupy the flight deck jumpseat.