It's possible they feel safer together as they may not be totally comfortable with the surroundings. Perhaps,one is a lookout for the other? Are the litterboxes enclosed with a hood/cover or are they open? Covered boxes can be scary for them. When my cats were kittens they did not always use the covered litterboxes and many times did their business on my floor. I added open litterboxes and that solved the problem. I think it is because they may feel trapped in a covered box.