I think I know what the problem is! I think you are selecting the wrong device when Nintendont starts up. Pick one, and if it doesn't show anything, pick the other. You are supposed to pick the device that has the games, not the device that has the Nintendont data.
Another thing that might fix your issue is to make sure you have the titles.txt that goes in the nintendont folder. If not, you can download it in Nintendont internally, or you can pick it up here:
https://raw.githubusercontent.com/FIX94/Nintendont/master/nintendont/titles.txt
You just click the link, then right-click and click "Save Page As..." and save it as titles.txt. Plus, if you already have it, it wouldn't hurt to update it anyway.