Whenever a dog develops a persistent lameness at a young age there are are certain congenital and developmental problems we must look for. Elbow dysplasia, shoulder joint surface problems, panosteitis, are some of these. When the original problem occurred there may not have been changes obvious on x-rays. Things may be different now and retaking x-rays and comparing to before may be helpful.
Keeping him confined is appropriate for some problems, but for others there may be a better way to handle it. I think it is important to get him rechecked and get a diagnosis so you will know what to do and if it will affect his quality as a breeding dog. If you can go to an orthopedic specialist that may be best, XXXXX XXXXX vet about a referral.
Depending on where you live, testing for Lyme disease may be a good idea. Here in New England it is something we must always look out for.
I hope your dog feels better soon.