Black Balled!
Well, jetBlue has a reputation of black balling people. Perhaps someone he worked with at Independence who now works for jetBlue heard through the grapevine that he got hired then went to the people department and said he had a problem with this person working at jetBlue too.
OR there IS something sinister in his background.
OR, as I've heard before, after many, many months of waiting just to get phase 2, they decide 'no' to phase 1.
OR, maybe the applicant is not being truthful. What airline ever discloses the reason they don't hire someone? Hummmm......