Milk intolerance?

My baby is 11 weeks old and has been on three formulas.  First was Enfamil Newborn, she had gas all the time and really bad diarehhia.  She then started on Enfamile Gebtkease and got constipated.  She has been on the Reguline for like a month. She was pooping once a day or once every day and a half.  Last Sat it changed.  It's no longer one big green poop.  It's yellow and runny several times a day. 5 times Sat 2-3 times all week. 7 times on Wed. 5 so far today.  And it has been during eating or shortly after. 
Do you think she has a tummy bug ?   Or I question a milk intolerance.  She has eczema. So do I, so it could be hereditary but it's super flared today.  Sometimes she makes this noise in her throat like a tickle.  Her eyelids are red.   If it doesn't change over the weekend I am calling her doctor.  He already told me to switch her to soy if she kept being fussy but that has changed a little.  Oh and prior to all this poop, she had awful loud, smelly farts.  People would comment on how bad they were.  :(