If its only one leg bothering him then this might be due to 'growing pains' which can be due to a number of issues. You can read about those here
http://www.labbies.com/dysplasa.htm
on a page put together by a labrador person but it applies to large breed pups of any breed.
But if he reacts no matter what foot you handle he may just have sensitive feet and need work on letting you handle them. You might find this article on teaching good behavior for grooming useful
http://www.clickersolutions.com/articles/2002b/grooming.htm
or this one on nail trimming
http://www.clickersolutions.com/articles/2001/nailtrimming.htm
But you may be seeing joint pain due to the extra calcium you are giving him. You might want to taper this off giving a little less each day and see if glucosamine chondroitin such as Cosequin does a better job of helping the ears go up. Glucosamine is used in cartilage production and the ears are cartilage.
Typically ears do go up and down while a dog is teething.
Hope this helps you!
Dog Expert:Rescue, Train,Breed,Care
30+ yrs dog home vet care & nursing, rescue, behavior&training, responsible show breeding, genetics