The chanty does not appear in Hugill, and may not have even existed when Shanties From The Seven Seas was first published in 1961: Bob Walser's sleevenotes for his album Landlocked, state: "According to Ian Woods, the late Angus Russell was the source of "Skipper Jan Rebeck". If Angus wrote the song, as some people think likely, I think he would have been pleased to have folk think it was traditional."
Jan van Riebeeck was born in 1619 in the Netherlands. He joined the Dutch East India Company as assistant surgeon and was posted to Batavia, the present-day Jakarta. After service in Japan, he was put in charge of the trading post in the Tonkin region of Vietnam, but was recalled to Holland when it was discovered that he had been doing some trading on his own account (perhaps selling tea in Carolina?). He eventually regained favour, and landed with three ships to set up a staging post at what is now Cape Town to enable ships bound for the Indies to take on supplies of fresh food and water. Up till then scurvy had been a huge problem on long voyages with death rates of 40%, but it was known that recovery was quick once on shore. Wine was also known to be better than water for preventing scurvy, so he imported vines from Europe, with the first pressing in autumn 1659. After 10 years as Commander of the Cape, he continued his career further east, being promoted to Secretary to the Governor-General of the Dutch East Indies . His wife, who bore him eight sons, died in Malacca in 1664 en route to this new post, but he lived a further 13 years, dying in Batavia in 1677, at the age of 57 without returning to the Netherlands. His son, Abraham van Riebeeck, was born at the Cape and later attained the rank of Governor-General of the Dutch East Indies. Jan van Riebeeck's significance in South Africa remains huge, with many Afrikaaners regarding him as the founding father of their nation. Up to the mid-1990s, his image appeared on bank notes and postage stamps, while April 6th was a public holiday, known intially as Van Riebeeck's Day, and recently as Founders' Day. Many towns have streets named after him, and there is a statue of him and his wife in Cape Town. The city's coat of arms is based on that of the Van Riebeeck family.
I learned this from The Hardtackers.