Hi, I'm coming into this thread rather late, but I thought I'd relate what I'd come across in my own research that might shed some more light on the OP's family story.
The question is why were they there in the first place? The only thing I can find about that time is the gold rush.
Would ordinary working class people really go to seek their fortune? Charles Henry's occuption on the 1881 census is engine smith.
Though there had been a signifcant number of British settlers arriving in South Africa during the 1800's thanks to some government aided immigration schemes (1820 Settlers in particular), the discovery of first diamonds in Kimberley and then gold in the Transvaal sparked a large immigration into the country.
There would have been a great demand for trades related to mining (fitters, turners, boilermakers, engineers). Two of my great-great grandfathers arrived here in the mid 1890s who had both been factory workers in the UK and came from very much working-class families.
But it wasn't only mining related jobs that enticed people - I have two great-grandfathers who arrived as farmers from Italy and Portugal around 1900 and started a profitable business as fesh produce farmers who supplied the mining villages that sprung up on the Witwatersrand.
So it wasn't so much that these people were 'seeking their fortune' in the way we always see American gold rush pioneers depicted out hunting for that elusive nugget of gold. They simply came over here to do the same kind of work/trade that they had been doing at home, but there were simply more job opportunities, and in a lot of cases better living conditions (the mines built a lot of housing around that time, and the climate in South Africa is a lot milder than most of Europe).
If he did go he wasn't very successful as in 1901 he is back in West Ham.
Given that date, it may have had nothing to with success at all. If he was out working in the gold fields of the Transvaal, he may have been forced to relocate when the second Anglo-Boer War broke out in 1899.
I'm presuming he was born there and then he and his mother returned to England possibly leaving his father out there.
I have a great-grandmother who was born in the Transvaal in 1898, but then I find her living back in Norwich (where her parents had come from) in the 1901 census with her siblings and mother, but her father wasn't living with them. Then she returned and lived out the rest of her life in South Africa. This puzzled me for a while, since it seemed odd that they'd returned to the UK without her father, and why had she come back to SA after that?
It was only when I found a compensation claim filed by her father in the National Archives that I realised what had happened. In his letter to the government, my great-great grandfather explained that they had moved here in the mid 1890's and settled in the Transvaal, but when war broke out, they were forced to abandon their home near Johannesburg, and he sent his wife and children back to England, while he stayed and joined the volunteer forces to fight in the war on the side of the British. The compensation claim was filed when the family had all returned home to Johannesburg after the war and found their home looted and damaged. They actually received reimbursement from the British goverment for that.
So in your case, perhaps the family returned to England at the outbreak of the war, but due to financial pressure/discouragement at the war/loss of property, they might simply have decided not to return as many other families did.