Here's a case where c. diff. exacerbates colitis and cipro/ flagyl/ vancomycin treatment improves both. The underlying ailment is UC, but it's triggered by c. diff. The study goes on to suggest that c. diff. is difficult to permanently eradicate, but vancomycin puts the patient into prolonged remission.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC548304/
You'll definitely need a new doctor, and stool samples wouldn't hurt. Vancomycin ain't cheap, either.