I'm wondering if it is like clostridum difficil, a nasty infection humans can get which is very resistant to treatment ... and often relapses. Its what killed my dad - they thought it had cleared, he moved to Texas, and he relapsed quickly, then passed.
Have they found anything infectious at all?
And for a shot in the dark, if it is some sort of pariste that is difficult to detect, what about adding food grade diatomaceous earth to his meals? Its relatively innocuous, so shouldn't hurt him, and if there are cysts or parasites, may help control or eliminate them, in addition to what other meds are on board. Do run that by your vet - I know they add it to farm animals feed to reduce the impact of parasites on the animals health.