i would find an animal communicator and communicate! ask your dog what's up!
i have a cat that we rescued (had been dumped in our neighborhood). at first she had this really bad habit of peeing outside the box... very different than your dog's issue, I realize. But... I called an animal communicator that I know. She told me "she's not the pee lady," and gave me someone elses name. I no longer have it, or I'd pass it on. My cat's pee problem was solved 99% in 2 sessions. Every long once in a while she still does it, but it is absolutely nothing like it was before.
the actual session with the communicator was alot of fun. i'd ask the question and she'd talk to our cat, and then respond back to me. was a blast. (and it worked).
If you don't know a communicator, there's always sonya from the animal planet. She takes phone consultations.
LisaG