The passages you are looking should probably be played F/F#°/Gm7/C9, though, in checking my charts, I am not sure quite what parts of the tunes you are talking about--anyway, in that kind of chord progression, the bass line is moving chromatically(by half-steps) and the F# is not in the key--it is written as an accidental--jazz melodies don't quite follow the rules of diatonic melodies, because, as the chords move through the circle of 4ths, so does the key of the melody--in other words, those accidentals really mean that you are playing in another key than the one you started in.