I really wouldn't worry too much. I've traveled through Dubai on transit quite a few times and have never had any problems like that, even with some over the counter medicine in my check in luggage.

I assume you are just changing planes in Dubai, so your luggage will go straight from one plane to the next. Given that you are not actually entering the country, and just in transit I really wouldn't worry about it.

For interest sake, where are you going in SA that requires malaria medicine? I live in Cape Town, and unless you are going really far north (to Kruger) or over the border into Mozambique you really shouldn't need malaria medicine.

Enjoy your holiday in SA, the weather is getting good now!