I personally think all puppies go thru their bout with the runs. Whether on meds, have a digestive situations etc, even healthy pups will IMO go thru the runs.
One major reason I do belive in stress. They are taking into a new environment, away from their littermates, etc. So that inconsistancy can cause the upset stomachs. Also the richness of the good food can take awhile for them to be aquainted with it. I think it take a good full month of being on a certain food to see any results. Many people are getting puppies that are on not so good of a diet. Why, because when you have multiple mouths to feed many of you would be buying the family back steak deals and not t-bones. So I think there is some transition time too.
Hanna had the worst runs when we got her. Everything internally was fine, but just had to rotate around and find the right food. Not soo cool with off white carpets and a dog with the runs. About 3 months we finally found the right food. Canidae was a perfect fit. One is was cost friendly, yet still had grains that allowed her system to bind up creating glorious nuggets after months of pooppaste. Like another post, it like winning a new car when you see your first solid duke.
So just give it time, be patient and you will find the right things that agrees with your boxer's belly. However its always easier when the breeder is feeding the good stuff - Kash I have never had the runs with - for that I am one happy mommy!!!