What are you using to sand the corners with. Box joints have an situation where you are sanding side and end grain at the same time. If your sanding backer is soft, you may be sanding the side grain deeper than the end grain? Heat and moisture can contribute. If the wood is not completely dry, the side grain fingers will shrink and the ned grain will not. If you get a higher humidity, the side grain will swell but the end grain won't.
Do you have pictures with tangential lighting that shows the unevenness?