I have noticed a bug in the tool that if your start and end points aren't the same then it does mess up the pricing.

For example I was looking at ex DOH finishing up in DXB and the base price was way over the DOH figure. When I changed only the last sector to end in DOH and no other changes the tool priced the routing up correctly.

Doesn't really help the OP a lot as you can't re-route back to South Africa.