My horse has been this way for years. His poop is normal, but there is always some runny discharge with it. The bottom line for him is that he seems to be sensitive to ANY diet change. This includes hay, from bale to bale, when the grass changes for any reason, season to season or day to day because of heavy rain or lack of rain. I have talked to more than one vet and tried A LOT of different products, from over the counter to prescriptions, but nothing changes it. The advice I was given from one vet is that it really is not all that uncommon. As long as my horse is healthy and not showing any other signs of being sick or in any discomfort, this is just a part of who he is.
If this just started happening recently, it may just be something in this years hay. Horses have very sensitive digestive systems and one little thing can upset it a bit.
It sounds like you have talked to your vet, as he took a fecal sample and it came back clean. Watch your mare, keep your vet in the loop and do not let the internet scare you silly. I did and probably put my horse through a lot of unnecessary medications and supplements.