Hi honey,
When my son was born, he weighed nine pounds. Within 3 months, he was down below his birth weight. No one could tell me what was wrong--just that I wasn't nursing him enough. Gee thanks (I was).
I ended up taking a stool sample to a vet (that's veterinarian) and having it tested for parasites. He had very smelly, runny green stool. Turned out he had giardia. Yes, giardia. No, my son did not go drink out of a stream right after he was born. I had apparently contracted it some years before, still had it, and passed it on to him.
The moral of the story is...clearly you know there's something wrong. When the mama's radar goes off, don't let anyone tell you otherwise. Do what you need to do.
If she has bad smells from both ends and isn't growing as fast as you think she should, keep digging.
If your doctor won't have the lab check out a stool sample, I would find another way. Hint, hint, hint....
I would check for parasites first. My son had his first dose of the anti-parasitic medicine and started gaining weight immediately (on my "inadequate" milk) He put on over a pound a week for two months and then leveled off like a "normal" baby.
Yes, the mention of probiotics is good. Avoiding fluoride in any form, genetically modified foods, and using some cleansing herbs would be wise. If I can do anything to help out, feel free to message me directly.
Best wishes and blessings to you and your daughter.