Did they do a fecal or blood work? I'm not an expert on reptiles but just from looking at the xray I'd suspect some kind of impaction or parasites. There could be a cyst, do snakes have hormonal issues? Or maybe it is a foreign body that has tissue built up around it?
Antibiotics won't hurt, there's infection somewhere. I normally lurk but thought I'd throw out more suggestions since your vet is stumped. A MRI is a good suggestion, I'm sorry your snake is sick. I hope they figure out what's going on.
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