I was going to suggest a urinary tract or bladder infection, but it sounds like they've already tested him for that. It could be "just a virus." My doctor told me (at our most recent "what is this random fever" visit) that a fever isn't such a big deal in kids, as long as they're acting fairly normal. If they're lethargic and sleepy and can't seem to find any energy to do anything, then you have a problem.
I know it's frustrating. My 4 year old just came off of a 3 day fever thing. "Just a virus." They ought to just put an ATM in the lobby where you can put your Visa card in, and a recording can say, "It's just a virus, keep doing what you're doing, 7 - 10 days, blah blah blah." It would save the doctor a lot of time. :)
A. @ http://prettybabies.blogspot.com