Theres not much info I have been able to find about whether or not Border Patrol is conducting polygraph examinations on applicants. However, having experienced it first hand I can inform those who may have been wondering that BP is in fact conducting polygraph examinations to circumvent actual background investigations. During the interview I was told that at this time not all applicants are being examined, just a certain percentage. I happen to be one of those lucky few. He also informed me that within the next year they will be attempting to polygraph every applicant.
Their job is to get you to admit to something. Without an admission they have nothing to go on.