Reading your post you sound as though you have the same issues we had with Abbi.. Our 5 year old cocker had been like this for the first couple of years of her life. We had tried various different foods, both dry and wet with very little improvement. We'd been to the vet numerous times and they had said it was colitis and suggested diet changes. Eventually they put her on Hills ID diet which was expensive but we didn't mind if it worked, but she wasn't great on that either. The last resort was going to be blood tests for intolerances to different foods. In the meantime, with the help of some of my COL friends, I had been looking into the benefits of raw feeding and how it has helped dogs with colitis. I mentioned this to my vet but he said this would be too rich and make it worse. I decided that I had nothing to lose, as none of the other foods were helping either and my vets bill was in the hundreds now. I switched her to a raw diet, ready made (Natural Instinct or Nutriment in our case) and within 2 days she was a different dog. This was 2 years ago and we have had no sign of colitis again. It used to be a miracle if her poo was normal but now this is the norm, and poos are far less frequent and tiny! Also she used to be reluctant to eat most of the time (probably because she knew it was going to have that effect on her) whereas now she wolfs it down in no time.
I know raw feeding isn't an option or choice for some people but just wanted to let you know how it has helped our cocker, with possibly a similar issue.
A lot of the commercial dry and wet dog foods have ingredients that a dog's digestion is not designed to cope with and this causes the upset tummies.
Have a look at
www.whichdogfood.co.uk as this gives a good breakdown as to what is in each food and treat.
There is also a TV programme on Channel 5 this Thursday at 9pm which is covering what goes into our dog's dinners.
I do hope you can get your puppy's tummy sorted as I know how upsetting it is to see them like this.