Did you have Johnes disease diagnosed by a diagnostic center? Most vets do NOT know goats... in discussing with vets, I've had to supply several of them with the information that Johnes is not known to cause diarrhea in goats. Johnes positives do have a depressed immune system so perhaps they are more likely to get diarrhea for otehr reasons - by far johnes positive animals have solid poops.
Not only do I maintain a Johnes free herd, I have worked for a few years at MSU's DCPAH where I can pick the brains of people who are familiar with Johnes. I do lots of my own research on my own time reading up on publications, and have also done undergrad research in the Molecular Pathogenesis lab here at Michigan State U with Johnes disease.

I like johnes, lol. I actually applied to Wisconsin-Madison as one of my schools of choice for Vet School mainly because of my interest in Johnes... well, and because I also like Dairy.
I'm at work now (MSU's DCPAH) and just asked the man who does johnes setup and has for years now - he's never even had a johnes positive diarrhea from a goat.

Cows, yes... Every johnes positive from goats has been PELLET feces. Most publications I look at mention that diarrhea is not really a symptom of johnes in goats in most cases.
Merck says no diarrhea with goats (look under paratuberculosis) :
http://www.merckmanuals.com/vet/mana...20goats&alt=sh
Here is their article on COWS:
http://www.merckmanuals.com/vet/gene...erculosis.html
Johnes.org is a GREAT resource for learning about Johnes. Johnes.org says that diarrhea in positive goats is not a common symptom.
If you suspect a johnes problem in your goat herd, the only thing to do is start testing, managing the disease for elimination, and strict culling. If you'd like help with any of that, I would love to help answer your questions and direct you to research, testing facilities, and interpretation of test results - because no one test is definitive and due to the way mycobacteriums work, the elimination is a long drawn out process. Johnes disease is incurable. To start, I'd probably do ELISAs on blood and pooled fecal cultures. Necropsy if one dies.