Okay, when it comes to ailments of horses, I'm usually not the go-to person. (Cats, Dogs, Birds yes, Horses - Nope!) However the mention of a wonky gait reminded me of a problem a friend had with her Tennessee Walker last year. Unfortunately I don't remember all the details, names, etc... but it was an inherited nuerological condition (and incurable, in part, because it had gone on so long). She said the vet had to do specific neurologic tests to discover it. The only symptom I vaguely remember is the way the horse held her tail and the funny little kick out thing she did mid-stride. This horse was barely 2 and had not been riden, which I'm guessing is why it wasn't noticed sooner. It seems like she said this was something that was breed specific -- so it might not apply.

I'm hoping this is not the case with your horse, but has the vet checked for neurological conditions? Others may know what I am talking about and shed more light on the situation.