This whole chord/melody analysis business gets fairly messy most of the time. It usually takes a few go-rounds just to figure out what everyone is talking about, and to make sure that people are talking about the same thing--when that it out of the way, hours,days or weeks later, you get to the bottom of things and discover that it was all very simple all along--
I was once working with a singer on a demo of an old jazz standard, "Pennies From Heaven"--and we were working from the some very cool jazz charts that someone had gotten from somewhere vaguely famous(though where was never really clear). The voice sounded good, the instruments sounded good, but together, it was bad news. We went at it for hours, getting madder at one another by the minute.
Finally, someone noticed that there was a chord progression based on a dominant seventh chord where there was a major seventh in the melody--so we were playing two notes, a half step a part when they should have been the same note, and any dummy could have seen it--