Did you assign a bank preset to a track mapped with Kontakt.
-Click right a track with a kontakt map
-Choose plugin preset/new bank library
-See that the new bank library preset is assigned to a kontakt track
-In the preset pane (left) click on Sync
Now podium will save the entire kontakt setup with the *.pod file
If Kontakt is set as a global plugin and you use different tracks mapped with different channels to kontakt you only have to set a bank library on just one kontakt mapped track.