It sounds like the second vet is being very thorough. I have dealt with similar issues but in a much older dog. Some of the medicines your pup is on can cause the lack of appetite. I have used nutrical (I think that is the name) to boost appetite and give the dog more calories.
It sounds like they are treating for a lot of different things since they aren't sure what the problem could be. After Frieda's MRI, the vets said it could be IBD, cancer, possibility of her chronic fungal infection migrating to her organs, and a few other unlikely things. Because of her age and her chronic condition the vets advised against exploratory surgery and other treatment.
Your pup is much younger, and it sounds like the vets are doing a very thorough job. I hope the problem is figured out soon.