Take a sample of them into your doctor or hospital if they are not returning to a more 'normal' state for her.

Charlotte had gastro a few weeks bad quite badly, which cleared up, only flare up again a fortnight later for no apparent reason, with no vomitting etc, just the terrible poo, gut aches, cramps and lots of stinky farts. I ended up taking her to the hospital after quite a large amount of blood in one and had the sample tested - turns out she had a bowel infection - it cleared itself, but affected her for about 4 weeks or so all up.

ETA: Lactose intolerance in a BF baby is very rare, as when you are breastfeeding, the baby produces Lactase, which breaks down the lactose in milk. Once you finish breastfeeding, this enzyme stops being produced and that is when you will get lactose intolerance, allergies etc..