OMG, those ducklings are too cute with those socks! It is interesting that your Pekins had more of a problem then the Mallards. What are you feeding them? I had a few issues this summer with what I would consider relatively minor foot issues (compared to something like a bad case of bumblefoot). Some cracking (actually quite a bit more than some) on the bottoms of the feet is completely normal. Some of the experts, like Holderread's, definitely say that it absolutely can be a result of a Niacin/B deficiency.
This is the first year that I have raised birds start to finish on Flock Raiser and it is the first year that I have felt like we had more cracking then what is within the realm of normal. Interestingly though, it was predominately in the Welsh Harlequins. Our smaller birds that we raised on FR, like a bunch of Mallards we raised and some Runners, none of them had it (excessively). When I added a vitamin supplement to the water, the cracking literally immediately began to improve. It makes me think that maybe the Niacin level in Flock Raiser is adequate, but not optimal (and obviously that could apply to other feeds as well). It would be entirely possible for it to be fine for some breeds and inadequate for others.
Anyway, I am not sure what you are feeding. I am just thinking out loud about what may be the source of the problem. I think getting them on the yeast is a great idea. After all the feeds I have tried over the years, my ducks have never looked better than when they were on Purina duck chow. It is a shame that it is so hard to get and that so many feed lines have gone to these triple duty type feeds.