Had the same problem after installing Obsidian with AppimageLanucher. The solution for me was changing from StartupWMClass=Obsidian to StartupWMClass=obsidian in my obsidian.desktop file. Also my obsidian.desktop file for some reason isn’t located in the usual /usr/share/aplications folder but in /home/USER/.local/share/aplications.
Setup:
Obsidian in version 0.8.4 (AppImage)
System: Ubuntu 20.04.1 LTS
Gnome 3.36.3
AppImageLauncher-Version=2.1.3