Only just seen this, Nic, and can fully sympathise.

It sounds pretty much what Mocha was like at the start of last year, although her shoulder was actually luxating so there was always an obvious problem when she went really lame. After 3 weeks of onlead exercise only with no improvement, the vets took x-rays which showed nothing wrong - joints were all perfect, no signs of arthritis. We were then referred to an orthopaedic vet who took more x-rays and did a joint tap, still showing nothing. He basically came to the conclusion in the end that her ligaments and tendons are "loose" and don't hold the shoulder joint in place, that's why it kept luxating. There wasn't any surgery to do, so it was basically lots of hydro and restricted exercise. She was on the lead for 6-7 months in total and it was a nightmare. She's pretty OK now, but once the muscle tone decreases around the shoulder joints, she goes lame again.

I know Tilly's incredibly fit and already swims lots so she'll be really well-muscled.
Anyway, hope the vets come up with something soon and that it's nothing serious and can be easily treated. In the meantime, I'll be thinking of you and your increasingly frustrated brown dog.
