In the last scene, where it counts down to the year 2000, you can see a sliver of the clock in one scene and it reads 51, 52 seconds. In the next shot, a close-up of the screen, the seconds are at 43. See more
Mulder, these people, even when they were alive, mangled biblical prophecy to the extent that it's unrecognisable. The year 2000 is just their artificial deadline, and besides 2001 is actually the start of the new millennium.
Nobody likes a math geek, Scully.