Well I'm unsure what happened because I didn't clear cookies but my save is gone so. I'll just play again and if I experience it another time I'll notify you.
I appreciate you putting the time and effort into trying things out and letting me know what happens.
I made another post above about the lost save files: unfortunately, updating the game has meant the old versions saves got lost. There is a potential work around to skip the prologue (explained in the post), so hopefully that helps.