The problem is still here but I discovered something Strange.
On relaunch the shortcut stops working but if I run the filter from the menu it shows up as the most recently run filter with my shortcut next to it ?!?!
Heya bumping this topic as well. Same thing is happening to me when recording a shortcut for RMX Tuner. Works fine until relaunching the app. Running 3.0.3 on 12.0.1 (21A559) With M1 Chip
Can you try to add a shortcut in System Preferences > Keyboard > Shortcuts > App Shortcuts. That should be visible in the menu immediately. Restart Glyphs and change the same shortcut. Then restart System Preferences and check if the new shortcut is shown there, too.
Hmmm no luck :^/ It’s not the end of the world but having a shortcut for RMX Tuner is kinda baked into my muscle memory now. Having to click through the menu is somewhat disruptive. BTW it also doesn’t show the filter when using CMD+R after previously using it. Works fine with other filters.