Why is the Geneva Bible the only translation that I have found that translates Genesis 1:9 as
The Geneva Bible of 1560 and 1599 was the Bible of the Protestant Reformation era. It was one of the earliest translations of the Bible into English, but not the first and not the last. The Tyndale New Testament appeared in 1526 and the King James was translated later in 1611. The Geneva Bible was used by John Knox, John Donne, William Shakespeare and John Bunyan, author of Pilgrim’s Progress. It was transported to America on the Mayflower.
Brief History of the Geneva Bible
The Geneva Bible is printed by a number of publishers today. Here is a brief history from the Hendrickson Publishers.
Sixteenth century English Protestant scholars were determined to make the scriptures understandable to common people, so that, as William Tyndale famously put it, “the boy that driveth the plough should know more of the scriptures” than the educated man.
However, Queen Mary’s (1553–1558) persecution of her Protestant subjects caused many to flee to the continent to avoid imprisonment or execution. Geneva, Switzerland soon became a center for Protestant biblical scholarship. It was there that a group of the movement’s leading lights gathered to undertake a fresh translation of the scriptures into English, beginning in 1556.
Published in 1560, the Geneva Bible’s popularity kept it in print until 1644—long after the advent of the Authorized Version (a.k.a. King James Version). It was an English Bible that met the needs of both clergy and laity. Perhaps the Geneva Bible’s greatest contribution was its commentary, which undergirded the emerging practice of sermonizing and helped foster scripture literacy. 
A more in-depth history of the Geneva Bible is provided by the publishers.
The Bible contained footnotes of commentary. The verses were numbered and words not contained in the original Hebrew and Greek texts were italicized. The Bible also contained maps. These features made it the first study Bible with Reformation doctrine commentary.
Translation of Genesis 1:9
In order to answer your question we must know the Hebrew text that was used by the translators. It is believed that the New Testament of the Geneva Bible was translated from the Estienne’s Greek New Testament of 1551 and Beza’s Greek New Testament of 1556 or the Textus Receptus. The Old Testament was translated from the Masoretic Hebrew text.
Since the Masoretic Hebrew text was used for translation by the Geneva Bible as well as every other major Bible translation since then, there is nothing unusual about the original source.
Therefore, why does Genesis 1:9 of the Geneva Bible start with “God said againe”?
God saide againe, Let the waters vnder the heauen be gathered into one place, and let the dry land appeare. and it was so. Genesis 1:9 (GNV)
The answer is that we cannot be confident. The word translated as “againe” does not occur in the Masoretic Hebrew text. Therefore, the translators added the word. It appears that they added the word “againe” since God had repeated His command, “Let there be . . .” The first time that God said, “Let there be . . .” was in Genesis 1:3.
Then God said, Let there be light: and there was light. Genesis 1:3 (GNV)
Then in Genesis 1:6, God said, “Let there be . . . ” a second time and the translators added “againe” at the beginning of that verse.
Againe God said, Let there be a firmament in the middes of the waters: and let it separate the waters from the waters. Genesis 1:6 (GNV)
Then they did it once more in Genesis 1:9. Then they stopped.
It appears that the translators of the 1560 and 1599 Geneva Bible wanted to remind us that God was the Creator. He commanded light into existence in verse 3. Then He commanded an expanse in the water in verse 6. Apparently, the translators wanted us to know that God created again. Then God created again in verse 9 when He formed dry land. Evidently, they wanted the reader to be reminded that God was actively creating.