The fact that you have been providing a duck feed, with added niacin, and have not noted any other similar symptoms within the flock might suggest the problem is genetically inherited and is not related to your husbandry practices.
Since niacin deficiencies are so common in large heavyweight breeds, it would not hurt to supplement the bird with niacin, and it may help with overall leg health as well. An injectable form of niacin can be found at your feed store - I suggest giving the duck 1ml daily over treats.
https://www.tractorsupply.com/tsc/product/durvet-hi-level-vitamin-b-complex
I cannot actually see much of the duck's legs from the pictures you provided, but from what you've described, and what I can see - it sounds very much similar to a varus deformity, which will cause the femur (hip area) to bow out, and the feet to cross over.
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Varus deformity, or bowed- legs can occur be due to genetic abnormalities, incorrect husbandry practices, and several mineral/vitamin deficiencies. Over the internet, I don't think anyone will be able to tell you the exact cause, but you may try treating for mineral/vitamin deficiencies, instead of just supplementing with niacin. Poultry Nutri-Dench, Poultry Cell, or Sav-A-Chick are all suitable products and can be found at your feed store.
Pekins are especially predisposed to leg problems due to their fast growth rate, therefore, attempts to lower the growth rate may prove beneficial. Decreasing the amount of daylight, and feeding a feed lower in protein should slow growth rate. Abrasions and sores can develop on the legs of ducks affected with a leg problem so efforts to practice water therapy daily, and when not in water provide a soft cushioned floor would be beneficial. If the legs are manipulate-able you could attempt to put a splint, but doing so when the legs are too stiff could lead to a loss of circulation to the legs.