Corrected entry: When Neo meets the Architect, the Architect mentions that the matrix was created 6 times. The first two were disasters, and a solution was found by the oracle for the 3rd version. That means the 3rd version would allow "The One" and a "Zion" to exist; this meant that "Zion" was created 4 times (3rd, 4th, 5th version, and current). The architect mentioned that it will be the 6th time they destroyed it.
sksallaj
7th Jul 2011
Correction: No there was always a Zion, the humans were simply waking up en masse necessitating Zions rapidly recurring destruction before the 3rd Matrix.
Phixius ★