Hi Jakub.
The path that sets up the V3 Guid mode is unfortunately on the query path and so what’s happening here is data is being inserted before it can be reconfigured. I have a fix for this in the next version but in the mean time you can work around this issue by adding the line:
var _ = db.Notifications.FirstOrDefault();
Into your app initialization once the DbContext is ready.
Apologies for the inconvenience and you’ll be able to remove this line when the next update ships.
Update: A PR to fix this is now up for review. https://jira.mongodb.org/browse/EF-163
Damien