Does hesitation in completing the prayer, prior to reciting the Fatihah, invalidate it from a jurisprudential perspective?

It appears you are afflicted with waswasah (whispers/obsessive thoughts), and its cure is to ignore it. Scholars have differed on the ruling regarding hesitation in interrupting prayer. Some have held that it invalidates the prayer, while others have held that it does not invalidate it, because the original intention remains, and this is the correct opinion.