Oh my gosh, how frustrating. I would have his stool checked specifically for giardia -- giardia, btw, can hide under scope so sometimes it takes several tests to diagnose is. What I wonder though is if he actually already *had* giardia, recovered, and is now suffering the common after effects that some dogs have afterwards (for months!). This is what happened to my Marcel - he had giardia as young puppy, and then had diarrhea that no vet could fix for MONTHS. I finally consulted a pet nutritionist and she put him immediately on a home cooked white fish/green beans/potato diet and *boom*, his diarrhea was gone in 2 days...we fed that diet for about 1.5 months and then switched to raw and have been feeding that now for years.
I'd get him on a probiotic like
Nature's Farmacy's version, which also has digestive enzymes. You might also want to try giving some Benefiber to see what that does, as it could help.
If it continues, I'd recommend the fish diet for a while to see if that helps.
Could also be IBS - has that been discussed by the vet?