I don't know if this is the way Watchowsky Brothers intended it to be, but, simply thinking in theorethical terms, if Matrix can emulate an entire reality, it can emulate the sense of memory itself, the perceptioon of time passing by; So the matrix can make everybody belive "next year" is 2000, "last year" is 1998, "current year" is 1999, and keep people in this stage forever.

Alternatively, they may have needed two or three human generations time span to make the matrix look and feel realistic to its "guests", in which case it would be more than 2799, I guess (since the Matrix has been reloaded six times).

I think the first hypothesis is more fascinating, but probably harder to make it fit properly in the plot.

My 5 cents.