When the architect skill is used on a solid companion cube, it will look invisible although it still is solid. The right side will also gain friction allowing mice to be able to climb it from the right side.

When used on an invisible companion crate, its appearance will change to look solid, though only the right side becomes solid.

http://atelier801.com/topic?f=6&t=791982

Explained in that topic.

A similar bug occurs with the earth symbol.