C.M.
I had a cat that we rescued as well. She started doing the same thing every once and a while a couple of years ago and it became more frequent. I also left a message on this website but didn't get a response. I am glad that your message got put out here on the main page. Anyway, to make a long story short what fixed my cats problem was getting rid of the box all together and now she goes outside and there hasn't been an elimination incident since. I don't know if that would be practical for you but you might give it a try. I had also tried what you did with closing her up with the box and all. That would seem to work for about a week then we would have another incidence. Good luck.
C.