Every time I restart the app, my custom keyboard shortcuts top working. They are still set correctly in the preferences, just don’t work. I need to manually re-set them (to the same value), then they work again.
This is in 3.1.2 (3151).
In the latest builds custom shortcuts stopped working altogether 
I’ll have a look at the shortcuts.
Do you use Glyphs’ internal preferences? I’ve had better luck with setting custom shortcuts in System Preferences, apart from RMX tools hijacking them sometimes they work fine.
I’m having the same problem.
@yanone To what command did you add the shortcut. And does it work properly when you assign it in System Preferences?