I followed your recommendation and saw all navigators in the XPagesExt.nsf. I then took my application and compared all application settings to those in the XPagesExt.nsf. I set all settings to the same value and voila, my navigator showed up. I then did it backwards to find the setting that made it show up. It was the "Application Theme". In my Application the theme was provided as "OneUIv2.1". The XPagesExt.nsf has it "oneuiv2.1". So it's obiously case sensitive at least for navigators. It wasn't case sensitive in previous ExtLib versions though.
Anyway, problem solved, thanks!