Apologies if this issue has already been addressed somewhere, it cost me a few hours so posting for visibility.
I recently had an issue where I made an FSM prefab and was using it on a few instantiated objects in the scene just fine (basic rect transform set anchored position FSM for UI transitions). After adding a menu that is in the scene always, not instantiated, I noticed the FSM was visually updating but not doing anything in the scene. This seems related to similar issues containing the "State not in FSM!" error and prefab FSM attaching - although builds are affected as well.
My solution for now has been to simply to leave the gameobject inactive then activate it the first time it needs to be used.
Hope this helps someone!