Tested on multiple saves without mods and fresh saves. On all of them, Fairies only got the negative interaction with Vampires and Spellcasters on fresh new saves. I tested 5 of my older save files from before enchanted by nature and none of the relationships started out in red.
I tried being a fairy and meeting spellcasters and vampires, I tried being a spellcaster and meeting fairies, and I tried being a vampire and meeting fairies.
In all of my tests, the negative relationship only happens in fresh saves.
