It may be that the shampoo is not effective in ridding him of the yeast, no matter how frequently it is used and you may need to go to an oral medication for yeast like Nizoral. Or the problem may be that the shampoo is resolving the yeast, but the underlying skin condition leave him at risk for recurrence of yeast infections.
What it sounds like he may be dealing with is a condition called atopic dermatitis. Atopic dermatitis (AD) or eczema is a long-lasting (chronic) condition that causes itchy inflammation of the skin and ears. It may affect any area, but it is usually affects the face, feet, armpits, trunk, and abdomen. It may be persistent or it may flare periodically and then subside. These can make a dog's skin itch and there may or may not be other skin lesions visible. Itching problems in pets can be difficult to diagnose and the history and response to medications tried are a very important part of figuring out the cause
Animals with AD have two main problems. The first is an abnormal skin surface (barrier) which leads to sensitive skin. The second is an overactive immune system that reacts to a variety of flare factors. Recognized flare factors include: dry skin, food allergens, parasites (fleas), infection (bacterial or yeast), and environmental allergens, like dust, pollen, molds, etc . When a flare occurs, your pet will itch more and may develop red, flaky, and/or infected skin or ears, as these areas are then invaded by bacteria or yeast. When these bacteria or yeast live there for a long time, the skin can develop secondary lesions and even become blackened and thickened. These secondary infections require a specific treatment to resolve and is separate from therapy to manage the AD. A test called a skin cytology can be done to look for these organisms that cause infection. If yeast is found and treated effectively to the point that it resolves,and if the itch is still there, your attention needs to shift to treating the underlying skin defect. There is a great new product called Allerderm spot-on which helps to repair the damaged skin barrier that these dogs have and helps to decrease their itch flare ups.
Since AD symptoms can be a seasonal or year round problem, treating them or the secondary infections at any given time, does not mean the signs are gone for good and the symptoms may recur throughout the year. Although there is no cure for AD, it's symptoms can be treated with a variety of therapies/medications. If recurrences are frequent, the focus must shift to identifying the specific triggers of the allergic reactions with things like skin testing or food trials and then practicing avoidance as best possible.
I would definitely recommend that you work with a veterinarian who understands skin disorders like AD and it's triggers. They can look his history and seasonality of itchiness, results of dermatologic exam and response to medications or diet change and put it all together. They will also be able to best determine the appropriate treatment plan for him based on his current condition and history of what has been tried and how he responded. If it seems you are not making progress, consider working with a veterinary dermatologist.
Below is a link to find a board certified vet dermatologist near you:
Good luck and please let me know if you have any further questions.