Some things hit the ear wrong. I don't know how to explain it. It's like layering a kick and then switching out one of the layers. Even just EQing one of the kicks can change the entire tone of the drums. When you know what kind of changes to make to a sound to get it to where you want it it's easier to just use vague terminology instead of getting into the fine details of exactly what is wrong with the sound. Maybe the volume envelope is too long or something, but saying it's boxy is a shortcut. Maybe they don't know exactly what is wrong with the sound.

Either way, if you are watching a producer and they say a kick sounds boxy, watch what they do to fix it and then you will know what they mean by boxy. Did they EQ a part of the kick or compress it? If you know what they did to fix it you will know what they probably meant. Or you could just ask them.