Melanie,
I answered much of this on the QA tonight, but I think it is significant that the C. diff was found on stool testing. There are different strains of C. diff, and not all produce the 4-cresol that would be detected via the OAT.
I cannot say for sure whether the C. diff was a false positive. Usually, a lab may report a false negative versus a false positive.
C. difficle is best treated via a cyclical approach (as you tried with the Flagyl). Go back to the clostridia module and look at the information for the McFarland article using cyclical dosing of Vancocin (vancomycin). I would also put this person on CoreBiotic from Researched Nutritionals, available from New Beginnings Nutritionals too – http://www.nbnus.com. I would use 2 capsules at night.
If he failed Flagyl, then the next thing to try is Vancocin.
Also, if he is married have his significant other tested too. Clostridia spores are very resilient.
Sincerely,
Dr. Woeller