@StevenCee I have had this problem for as long as flux has been around. I found that if I have it set to auto open on login, then I cannot have it also do the same thing with flux itself. Once I have it auto open at login, I can delete that and have it set to auto open within the app.
I also experienced that if I have it set to auto-open at login, I cannot get the prefs panel to appear from the many bar UNLESS I manually open Flux from the apps ƒ and then the menu pulldown works.
If I hav it auto open from within the app after having done the "dance" with auto-open at login, then th pull down menu for prefs works.
This "behavior" remains even with the latest beta version.