I Never have had problems with the female pups, but Thorn would actually do great for a week, then I'd look and see him leaving a trail of pee as he walked to the door....I told myself it was because of him growing, maybe his bladder was behind his body or something. He didn't poo in the house just pee. It took a few months before he got it under control.
It sounds like you are doing everything right with the crate. It may just take him awhile to realize how it works. I don't crate Morgayne, she is older though and can go all night sleeping on her bed next to mine. I just make sure I praise the heck out of her and make a huge deal when she goes out. She seems to have the hang of it now.