Antibiotics in general can cause people to get the runs and cause digestive distress, so it is not surprising. Are you taking probiotics as well? If not, I would. You should separate the probiotics at least 2 hours from taking the antibiotic so the antibiotic does not just kill off the probiotics.
Oh ok, well that's good. If you continue to feel worse, I would call your doc and tell him about it, tell him you do not want to continue with the cipro if it is making you worse...