Dogs don't get flu which is a respiratory virus, and neither do they get the traditional rotaviruses which cause diarrhea in humans.

There is a possibility your pups could have a touch of Distemper. You didn't state how old the pups were, but sometimes the first Distemper shot doesn't take hold or only provides partial protection due to the interference of maternal antibodies. A blood titer would answer or eliminate it as a possibility.

Another possibility is coccidia or another intestinal parasite. Your Vet should be able to nail this one with the fecal sample.

My two favorite ways of giving pills are:

1. Wrap in melted cheese. It goes down usually in one gulp with no attempt to chew.

2. Hide it inside a peanut butter coating.