Leo there are a lot of people with wakeboard related shoulder injuries. I had surgery 6 months ago to repair mine and about 3 weeks ago it popped back out for the first time. My friend also had a total dislocation that day for the first time.
My shoulder is really loose and would pop out every run just as you described. It's been a lot better since the shoulder surgery but I have been rehabbing it like crazy with strength training. Obviously it wasn't a total success but I'm still happy with the results. After dislocating it the last time out, I'm not going to ride again without wearing a brace to lock my shoulder down. I only seem to dislocate it when my body rag dolls and my arm gets above my head.
If you can, get an MRI so they can be certain what's going on. I've heard that once you mess up your shoulder, it will never fully recover and that certainly hold true with me. It sounds like your shoulder is just as loose as mine and I doubt physical therapy alone will fix it. Strength training should help though. Even if it doesn't fix the problem, it will definitely help your recovery times.