I think I might have an idea. It could be related to App Specific Shortcuts Lagging Behind
Could you please go to the about tab in BTT and click the "Export Debug Information" button? This will create a folder called BetterTouchToolDebug on your desktop. Would be awesome if you'd zip that & send it to andreas@folivora.ai
I think there might be some exception that doesn't happen on all systems, but the debug info might show me what's wrong.