what are you using to brush him? It might be causing the flakes. I think I might use the Zoom groom (curry comb I think is another name) maybe a few times a year on Flirt. That's all I do. I never thought Dobes really needed "brushing." The zoom groom pulls the dead hair out.
I agree Adara--I don't "brush" my dogs--a lot of time all that brushing does to short haired single coated dogs is irritate the skin. To remove loose hair I use a dampened terry cloth towel and wipe the dog down. Also if you insist on "brushing" the dog get a natural bristle, VERY soft brush to do it with--the brushes used for polishing shoes will work for that.
I'd stop brushing him and at six months I start giving puppies fish oil (I don't recommend using cod liver oil--it contains so much Vitamin A that you can overdose a dog)--I get the fish oil I use from Costco--under their Kirkland brand--make sure you don't buy the enteric coated stuff--GI tract is too short in dogs and it often doesn't disolve--the stuff I buy is not enteric coated, is 1,000 mg gel capsules that I just toss into the dogs breakfast and dinner. It's still under $10 for 300 capsues as I recall. I'd start a dog on 1 capsule a day and in a couple of weeks up that to 2 capsules. I also give Vitamin E (also from Costco, Kirkland brand 400iu gel caps) at the rate of 200 iu per 1,000 mg of fish oil.
Puppies do go through multiple coat changes in their first year so part of the problem may lie there and seasonal change from summer/fall to winter may account for some of it too.
I don't know about the food--I've never had a dog that didn't do well on Purina's ProPlan Sensitive Skin and Stomach (Salmon and Rice) The fawn dog was weaned on it but not all dogs do well on the same food. Some of the very high end foods that I've tried out from time to time left the coat on two of my black dogs looking like a blackboard surface--dull beyond belief.
If Gunner was doing well on the TOTW pacific stream I'd probably put him back on that but if the coat problem started before you changed foods I'd be thinking about also adding fish oil. I know that some friends with Dobes who feed a food they liked so much that they finally became distributors for it to guarantee that they wouldn't have to worry about running out just doesn't have enough fats/oils/Omega 3 fatty acids in it during the winter so they suppliment with fish oil during the winter months.
And even if you only bathe when absolutely necessary I'll remind you that keeping the water you use at very cool temperatures will definitely help prevent flakiness.
Good luck on tracking down the problem.