Her bladder may not be as developed to hold her pee. I know it is a aim for you, but you may need to wake up in the middle of the night or the her out for last or later n see if that helps. You are cleaning out the crate w something that removes the scent, yes?
Have you explored the possiblity of a UTI?? Dogs definately care and by nature do want want to be in their own puddles.