reporter: tonight, the faa now investigating yet another disturbing runway close call, this time at boston logan international airport. the faa says on monday air traffic control told the pilot of a learjet preparing to take off to wait as a jetblue flight landed on an intersecting runway. cleared to land four right jetblue 206. reporter: instead, the faa says, even though the learjet pilot read back those instructions clearly, the pilot proceeded to take off anyway. the jetblue plane taking evasive action, going from 87 feet back up to 3,900 feet, before circling around and finally landing safely. jetblue 206, go around. reporter: tonight, the faa wants to know how close the planes got. when we have an error like this, very often it s a human error. and even though we had backup systems that operated here, the tower operator telling the others to go around, it s still too close. reporter: this as the faa faces tough questions about airline safety. abc news following at l