There are just a few things I wanted to add to this thread.
Some parasites do take longer to treat, and don't show up during every culture. Somethings like giardia or coccidia can also be hard to diagnose in some cats. The cysts for giardia are very hard to detect, again, the same when testing for coccidia.
Also, since you mention it begins again, could it be a tapeworm reinfestation, that occurs when your cat eats a flea. Check the stool for white rice looking segments. If that is the case, giving a monthly flea medication should help.
It also could be Giardia, which can easily be caught again if any of the shedding cysts remain.
It could also be that the kitten has had an upset stomach for so long, that the bowels are continuously inflamed and is continuing the diarreah. My vet has suggested childrens immodium AD to help the bowels relax. It has helped in some cases. If you choose this, call your vet first to get an accurate dosage according to weight.
If the tests continue being negative, you might need to look into the possibility of it being IBD (Irritable Bowel Disease), it can be treated with a special diet.
There is also something I have been hearing more about in kittens/cats is a parasite called Tritrichomonas foetus or TF. This link will give you a little more knowledge about TF.http://www.maddiesfund.org/organizat..._vet_diar.html
It may also help to contact a feline vet that may help to figure out something more.
Good luck, I hope things get better for you soon.