Lactose free milk?

Ok it took the doctors 2 months to find out my son couldnt drink regular milk or soy milk. Well now he has had runny bm for a week now and I thought it was just a virsus but its been too long. I called the doctor and thats what they told me to wait. Well during x-mas we bought 2% lactose free milk because they had no whole and I get wic and have to get alot and they said I had to wait 3 days for the next load. Could the 2% be messing his system up? Has anyone else had this problem? I thought it would be fine because its just less fat in it right? Oh yeah he has been on the whole milk for 2 months and is fine. Thats the only symptoms he has are runny bms.