When Guinan was ripped from the Nexus in "Generations", part of her was still left there. She told Picard she couldn't go back with him because she was already there. The part of her left in the Nexus, a place where time had no meaning, gave her her sixth sense. This explanation was in the original Generations script but was later edited.
GUINAN : It took a long time, but eventually I learned to live with it. And I began to realize that my experience in the Nexus had changed me...I knew things about people...about events...about time...
PICARD : Your "sixth sense"... I've always wondered where it came from
