I'm just a lowly PPL and probably have no business chiming in with this thread, but I'm a little naive about the whole thing and how it works.
I understand that the Captain has discretion about who he/she allows in the JS. If Airline A has a JS Agreement with Airline X, Y and Z, and pilot from Airline Y wants a ride on Airline A but said Airline A Captain has a personal agenda he's carrying out, doesn't that violate the JS Agreement between said Airlines? In retaliation, a Captain from Airline Y that has heard about this denies previously agreed upon privileges to pilot from Airline A. Then won't this whole thing turn into a battle between the airlines to the point that JS Agreements are rescinded?
Absolutely. You make a great point. Our Jumpseat Coordinator (furloughed TWA/AA) worked long and hard for us to have agreements with virtually every U.S. carrier, and one bad apple could topple any of them.
Back at my first airline, Atlantic Coast, we started a transition into Independence Air. Due to our agreement, we were still flying as United Express for 6 more months. A UAL captain decided to give me the boot on the very first day of IDE flying, saying that our airline "sold out" United. (Actually, United sold us out by demanding that we fly for lower rates that would ensure our pilot group took a pay cut.)
This was in spite of the station manager explaining to him that I was still a United Express pilot and eligible for the cockpit jumpseat. He made it clear that is was his own personal agenda. I felt bad for the FO who had to fly with him. Guess what? Since I called my ALPA reps and Chief Pilot right away, that CA actually put the j/s agreement at risk for the whole UAL pilot group. By the time he got to IAD, he was called directly to the Chief Pilot's office and given a nice reprimand. Many of those guys really wanted to continue to commute on us. In two and a half years of commuting, though, every UAL Captain I met was a class act, except that one guy.
Thankfully, I did make it to work that day. Guess who gave me a lift? jetBlue, an airline staffed by many furloughed legacy carrier pilots who actually do have a right to be bitter. Yet, they always greet you with a handshake, smile, and a ride to work.
To wrap it up, the only thing more pointless than Flightinfo.com is starting a jumpseat war.