Baby Poop and Formula..

So my DD (5.5weeks old) went from pooping 7-8x a day to once (and much thicker than before) with a little help from the handy dandy rectal thermometer after going fully on formula. After about a week and a half of the pediatric nurse telling me it's probably normal as long as it's not pellet-like I decided to follow my instincts and switch her to a soy-based formula. After just a day and a half she's back to pooping on her own... only problem is now (after a week) it starts off as hard and pellet-like (and like gray/green in color) and then turns into a mushy/runny consistency (and really yellow). I don't want to call the pediatrician (again) but I don't know if she's clearing everything out from the milk-based or if the soy is messing with her poor tummy.

Sorry it's so long just don't know what was better for her...