Captain Chakotay in Before and After had pips. With her dying breath Janeway must have promoted him to a real officer.... No one knew/remembered about the provisional ranks and Chakotay was expected to take over in Scorpion which is why Janeway gave the Indian that little leadership speach.
Mulgrew was being difficult much later and they threatend to replace her with John Savage. Am I to beleive that she had in her life only ever been difficult once?