Ok I sent you a pm about this but I looked up some information on it and thought I would post it here. I will just cut and paste the real pertinant information

Whipworms
Generally a dog's response to a whipworm infection is relatively mild, although exceptions do occur. Heavy infections can result in bouts of diarrhea and feces may be streaked with fresh blood. Young dogs or dogs with a chronic infection can suffer severe weight loss, dehydration due to diarrhea, and anemia.
Many dogs will carry infections of whipworms without much problem. Some dogs, however, will develop periodic smelly diarrhea which can become a severe problem. Large numbers of whipworms irritate the lining of your dog's intestine causing weight loss and pain. Whipworms are not dangerous to people, but once dogs become infected, whipworms are difficult to eliminate without medication programs. Large amounts of mucous are produced by the inflamed intestine. Sometimes hemorrhage into the intestine occurs and anemia can result. In very heavy infestions the worms may penetrate through the intestinal wall and the resulting inflammation causes the intestine to adhere to the body wall. Animals with this condition may frequently lick their right flank where the adhesion occurs.

Also, in dogs suffering from bloody diarrhea as a result of the infection, finding the eggs can be difficult.

A minimum of four fecal exams over a four-day period should be conducted before a negative diagnosis is made. Because of intermittent egg-shedding, a whipworm infection may not be correctly diagnosed. A follow-up exam may be necessary to rule out the possibility of infection.

Since the adult Whipworms may not lay eggs everyday, if your veterinarian performs a fecal flatation and looks for Whipworm eggs they might not be found. But the diarrhea keeps coming and going.