When farrier was out right after it started he said she had a mild case of laminitis but when he was back 8 weeks later he saw improvement in her feet, she did also have shoes for those 8 weeks.
I cannot be 100% sure it was the flax but it was just too high of a coincidence for me to try it again. Now I did pull all grain out and she is now fed as if she is prone to laminitis which this also completely solved her runny poo problem so perhaps grain intolerance as well.
Either way my dog is severely allergic to pretty much everything a dog should eat to survive so naturally my horse would have allergies too. Oh yea and I'm so allergic to hay that it brings on wheezing. We are a special family :)