Q) Can Janeway's ability be triggered by a free action given by a Flagship resource? E.g. Ind Flagship (Fed) permitting a free Evade.
A) Yes. Janeway's ability works anytime you take one of the listed actions on her card.
Q) If using Janeway to gain extra tokens from a free action (via the Flagship resource) and from a normal action, how many [Aux Power] Tokens are assigned to the ship?
A) In that scenario, Two. Each time Janeway's text is used to gain a 2nd token, an [Aux Power] token is placed by the ship.