Essentially, USCIS does not believe this relationship. Sadly, coming to the US and marrying after overstaying is one red flag. Marrying somebody who is locked up, is another red flag. Never living with the person is yet another red flag. Is he ever going to be released? If not, that's also a major red flag.
There's definititely suspicion from USCIS about geniuity of this marriage.
Overcoming it may be very difficult...
Are you originally from South Africa? There's certainly bias that comes with being from African continent, be it Egypt, Nigeria or other country.
This is "death by thousand cuts" situation, unfortunately.
Do you have a lawyer (sorry if I missed?)
Good luck and keep us posted.