Wow! So the earlier lists show Waldrons in Cape of Good Hope before the 1820s. I did a search of Francis on Google and in Family Search. Amazingly, there is a copy of "British Residents at the Cape" at the University of South Carolina Library not so far from me and I should be able to gain access as an alum. I have some work to do in Columbia this month and will see where that leads.
Family Search doesn't seem to find him from my searches there - not a Francis who is that far back, but I may not be digging deep enough.
I can only express my family's gratefulness to you all for your help. This has been a long-time mystery for the family and we pray for connections that make sense for Joseph Wallace Waldron. It is a unique sort of connection, for in all my wanderings over South Carolina, USA during his genealogical time period - both before and after, I have not found another South African immigrant - though there may be more that are not noted or misrepresented by census takers.
I suspect there is a story here about why he left South Africa for America, one that we may never know, but the search for Joseph's roots is a wonderful journey in its own right. And look at the new Geni-friends I have made!