I think I have found the issue and solved this, but I'm not 100% sure yet, need more testing.
After starting the game some times I suddenly got this error message from "SkyUI" when loading or starting a new game: Error Code 4: Your Papyrus INI settings are invalid...
I then spent 10-15 hours on this trying to figure out what was happening and I even started over again with fresh install of game, STEP, tools and mod organizer, but the same happened again.
After some time I found out that "Skyfalls" and "Main Menu Spinning Emblem" stopped working at the same time as I got the error message from SkyUI. If I then reinstalled this mods again everything worked well for some time until it all stopped again.
I started to think that it could be something outside the game itself since I had two STEP installations with the exactly same issue, and it seem like my own backup system have backfired this time. Due to loss of many hours of work some years back I implemented a heavy backup system, real time backup of small changes, hourly backup on important things like mod organizer folder, and daily image of windows.
So what I did was disabling all backup routines and stopping those programs. After I did this I have not received the error message from SkyUI anymore, and "Skyfalls" and "Main Menu Spinning Emblem" is working perfectly after starting Skyrim 15 times.
It seem like running hourly and real time backup on mod organizer folder some how interrupted certain scripts from running correctly. I dont know if this was because I played at the same time I did backups but that seem most likely, I dont know if it is the hourly backup or real time backup that is the cause of this issues, anyway it seemed to be solved now.
I need to test more to be 100% sure but at least I think I'm on the right track. It seem to come to a happy ending after all