again, it is always in the hands of the IO how they judge. You did nothing wrong on your part, the IO might feel that you do it not correct (in her eyes). Better to avoid that border and might follow her advise n use air for OUT/IN. Or another border near you.
due to unknown reason the Thai Embassy in Pretoria has written on the visa that this visa is for tourist purpose and future visa of any type need to be obtained from home country.
there is a border with Myanmar. They will stamp your passport OUT/IN, you no need for Myanmar visa, we do this run very often, for South African no issues.