I wanted to share a quick update, that I found a workaround. It seems, for now, that the problem didn't happen anymore since I use that, and I thought others might like to try this as well to mitigate the problem until a fix is implemented from the enpass team.
Here's what I've done (Note that I'm not native english, so some of the descriptions of apps/menu items/buttons are likely not exactly the same, as I translated them from my non-english UI ):
Disable 'Open Automatically at system startup’ option under General Settings of Enpass.
Launch 'Shortcuts' app on your mac.
Create a new shortcut with 2 actions:
Action: wait for 20 seconds (you can try more or less, but 20 worked well for me without annoying me, because it was not too long)
Action: Launch application enpass
close the shortcut
In the overview of all shortcuts in the shortcut app, right click on your newly created shortcut and select "add to dock". (can be removed from the dock later)
This will not only create an icon in your dock, but also an app in your users applications folder (e.g. /Users/johndoe/Applications)
You can add this new app to you "Login Items", so it's launched after you login. (optinally: remove the shortcut from the dock again, the app in your users application folder will stay)
That's it. Now every time you login, after a delay of 20 seconds, enpass is launched automatically. Whatever causes the initial bug why I opened this thread seems to not happen if enpass is lanched this way.
Some links if you struggle with the steps I described: (edit: had to remove the links to the apple support pages, as the anti-spam feature of the forum wasn't allowing me to post with the links. It's not too hard to find with google or similar though.)
Hope that helps