I dont know if this helps but I recently had a very similar problem with my 1yr old cocker. I did the same as you and sent a stool specimin (which came back negative) but luckily my vet gave us Anti b's anyway. Im not normally a fan of random courses of antibiotics without a proven infection, but I am so glad I listened to my vet on this one and it literally cleared up by about 2 doses in. The vet said that often they may have a bug but it just doesnt show up in the sample as they only test for 2 or 3 of the main ones. She also had blood in her poo and the vet said, the infection had caused a mild colitis.
I also switched her diet to Eukanuba dermatosis FP, again on the recomendation of the vet as its very hypoallergenic (fish and potato based). It was a bit of a revelation to be honest, and I have never looked back. Her poos are vastly improved, skin less itchy and dry, and fantastic coat. She also put back on all the weight she lost. Dont get me wrong its not a fantastic food and doesnt rate well on the all about dog food website, but she cannot tolerate a food that is higher in protein, just gives her the squits again. Initially I was going to switch her back to something else once the colitis settled but decided to leave her on it as she is doing so well. The other bonus is that because her main food source is very hypoallergenic, i dont need to be so careful with treats and have been able to reintroduce most stuff with no problems.
I also use a pro biotic (yumpro bioactive) and have found this to be very helpful as well.