I wonder if the two problems are unrelated?
Flagyl has antiinflammatory properties as well as antibiotic properties. If your dog has some malabsorption going on due to inflammation of the intestine, the flagyl could well make it better.
The lameness could be something else entirely. Are you in an area with ticks? If so, a screening for tick-borne disease might be in order.
Have you considered going to a veterinary teaching hospital for the bowel problem? Many Universities that have vet schools also have teaching hospitals. They see a lot of things regular vets don't, and they have good diagnostic equipment there that many regular vets can't afford. We had a young setter with similar digestive symptoms and finally got referred to the U of MN VTH. The diagnosis was inflammatory bowel disease. Our regular vet just didn't have the equipment to make the definitive diagnosis.
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