Liz Buchanan BVSc MRCVS
Hello- and its excellent that you are taking your dogs' oral hygeine seriously, even if it isn't the cause of the smell. This will have a preventative action and benefit your dog in the long-term.
Dogs can have smelly breath for other reasons- perhaps relating to strongly proteinaceous food, for example. In some animals, smelly breath can reflect an imbalance of chemicals in the blood, such as ketones in starvation or in the case of diabetes, or possibly in some forms of liver disease. Other times, they reflect the diet (some raw diets, some highly proteinaceous diets etc). Anal gland disease or diarrhoea (dog licks bottom, smell transfers), yeast infection in the skin around the mouth or ears can also sometimes be to blame, although your vet would usually have picked up on this by now. Foreign bodies in the mouth or diverticuli in the oesophagus, causing food to 'pool' in the throat or pharanx, can be a concern in some dogs.
Has your vet smelled the smell? This sounds to be a good place to start. Wishing you all the best - and please do let us know if you get to the bottom of it.