I have the same problem with Maggie Sue. In her case I think it is because she so desperately wants to be the dominant cat. She is too good to use anything that the other kitties use! That is the only thing we have been able to figure out. It isn't medical in her case. She will use it to pee, but most of the time she will poo right beside the box. It drives me crazy but I really don't know what to do about it. I try to tell myself that thankfully she is doing it in the utility room on tile and not the carpet or bed!!
The reason I think it is a dominance issue for her is because she trys to dominate the other two females all the time. She just has that attitude!!