I live in Rwanda and there have been many reports of Rwanda not letting you back into the country after having visited DRC even if you have a valid EATV. The reasoning is that the multiple entries are within EAC countries. So if you leave for Congo you will need a new visa again.
If you could avoid having to go through immigration at NBO you could get a transit visa in Rwanda and use the EATV to get back into Rwanda and then head to Kenya for Masai Mara.
Enjoy Nyarogongo and the gorillas, truly amazing experiences!