The problem here is that none of your players' buy-ins have a bounty chip cost yet. The interface DOES recognize a change in bounty chip cost and will prompt you if you change it, asking if you want to change it for everyone. However, there is one case where it does NOT change it, and that's if the player has a zero value for bounty chip cost. Since a zero value also means "the player didn't buy a bounty chip" (as opposed to "the player bought a bounty chip for $0"), the software thinks "this player didn't buy a bounty chip, so no need to change his/her bounty chip cost". Since no one in your tournament has a bounty chip cost, and thus nothing needs to be changed, you don't get prompted. (This would be important if, for example, only half of your tournament bought bounty chips. If you entered the wrong fee and later change it, you only want it to change for those who bought a bounty chip. You don't want it setting the bounty fee for those who didn't buy one in the first place.)
So, two options: (1) Edit the buy-in of each player and add the bounty chip or (2) Send the tournament to me and let me do it [programmatically]. If you have a small tournament with 5 or 10 or 15 players, no big deal just go with (1). If you've got a tournament with 50 or 100 players, send it to me.
For (1), go to the Players tab, edit the first player in the list, scroll down to the "Tournament History" section, double-click the buy-in and change the bounty chip cost. Repeat for all players.
For (2), send the tournament file to support@thetournamentdirector.net.