How about, the right hand doesn't really know what the left hand is doing. A lot of things went seriously lax under X42. My guess is that the ones directly responsible for the "checks" do cursory ones for the sake of appearances but never actually follow through because they know these people couldn't pass. I'm afraid our president has a blind spot in this area and it seems that both political parties have a vested interest in continuing to allow it and to push for this amnesty crap.
The same way Tyson was able to outfox the INS pilot verification program. Get somebody's real SSN, feed it into the system, and then have a fake SSN card/DL produced to match.