When logged in to two users, each running an instance of Flour, it seems that the Flour running on the suspended user still controls the Fn keys. You can reproduce it like this:

Log in to a user, start Flour and an app that you set to swap the keys. Now log in to another user while leaving that app open on the suspended user. Now try the Fn keys on user 2. They are now swapped as set by Flour running on user 1.

The intended behaviour should be that these settings are isolated per user, I think. You can't see from user 2 if user 1 has an app running that makes Flour modify the Fn keys.

Keep up the good work, loving it. ❤️
Greetings, Dane