OK, I'm going to try and give an unbiased explanation of this mishap.
In the first several drafts of STAR WARS, George Lucas had the time of the Republic's existance fluctuating between 1,000 and 100,000 years.
STAR WARS Rough Draft wrote:ROLLUP TEXT
Until the recent Great Rebellion, the Jedi Bendu were the most feared warriors in the universe. For one hundred thousand years, generations of Jedi perfected their art as the personal bodyguards of the emperor. They were the chief architects of the invincible Imperial Space Force which expanded the Empire across the galaxy, from the celestial equator to the farthest reaches of the Great Rift.
STAR WARS 1st Draft wrote:ROLLUP TEXT
Until the recent GREAT REBELLION, the DAI NOGAS were the most feared warriors in the universe. For one hundred thousand years, generations of DAI perfected their art as the personal bodyguards of the King. They were the chief architects of the invincible ROYAL SPACE FORCE, which expanded the King's power across the galaxy, from the celestial equator to the farthest stars.
STAR WARS 2nd Draft wrote:ROLLUP TEXT
Until the tragic Holy Rebellion of "06", the respected JEDI BENDU OF ASHLA were the most powerful warriors in the Universe. For a hundred thousand years, generations of Jedi Bendu knights learned the ways of the mysterious FORCE OF OTHERS, and acted as the guardians of peace and justice in the REPUBLIC. Now these legendary warriors are all but extinct. One by one they have been hunted down and destroyed by a ferocious rival sect of mercenary warriors: THE BLACK KNIGHIS OF THE SITH.
STAR WARS 3rd Draft wrote:ROLLUP TEXT
For over a thousand years, generations of Jedi Knights were the guardians of peace and justice in the galaxy. Now these legendary warriors are all but extinct. One by one they have been hunted down and destroyed by the sinister agents of the Emperor: the Dark Lords Of The Sith.
STAR WARS 4th Draft (Final) wrote:BEN: An elegant weapon for a more civilized time. For over a thousand generations the Jedi Knights were the guardians of peace and justice in the Old Republic. Before the dark times, before the Empire.
And, now, the contested quote:
Episode II wrote:PALPATINE
I will not like this Republic, that has stood for over a thousand years, be split in two.
As you can see, the only script treatment that agrees with Episode II is the third draft of A New Hope. I'm hoping that when Lucas goes for the Special Editions of the new trilogy he'll change it to /generations/ instead of /years/, but with him you never know.