when I run sudo geany it works, no popup.
I use geany since a while. In 18.04 I installed it sudo apt install geany. No issues to run it as a user. In 19.04 I installed the same way, but it seems to create the folder ~/.config/geany as root and that is why is not working.
I just checked ls -all shows root:root on the geany folder. Maybe something in the install script not working.