I believe the prevailing Chronoscholastic opinion here is that the Gates are not tied to absolute moments in time, but rather follow its linear progression just like we do. What remains constant is the amount of relative time between the two ends of a Gate. In other words, the gate at the Millennial Fair will always take you back exactly 400 years, whether you're using it to travel from 1000 A.D. to 600 A.D., or 1002 A.D. to 602 A.D.
One interesting question which I do not think has been answered is whether the endpoints of the Gates exist simultaneously across their entire lifespan in linear time. If you've waited around for two years and now it's 1002 A.D., you know that the Millennial Gate will take you back to 602. But if you were to use another time traveling device--a different Gate, or the Epoch, or something else--and travel back to 1000 A.D., what is not known is whether the Millennial Gate will exist at that time anymore.