You could have some degree of lactose intolerance, irritable bowel that seems to be aggravated by that. We do change with the pregnancies. I wore the same perfume for 20 years when I had the last one, it made me ill. Now there is one perfume that I can tolerate and I guess I will be in trouble if my system starts saying no to that.
You might want to try googling. I have seen several television programs with peope that were ill to the point that it started creating significant problems and they were able to find others and piece things together to seek treatment.
Also, you might want to try stocking up on lomotil. If I know I am going to be someplace like Six Flags, I will take it the night before and again that morning to make sure my stomach doesn't start acting stupid. If you know pizza is in your future, you could take it and see if it helps you enjoy the pizza without the aftermath; Wal-Mart makes its own version (interestingly enough nearly identical in appearance to the brand name product) but it works well.
As I age, the things that seem to irritate my system increase. Lettuce has always been iffy with me and like you, sometimes it seems okay others, not so much. It has gotten to the point that when I remember, I order tacos without the lettuce. I now seem to have heartburn the last couple of years fairly regularly when previously the only time I ever had it was when I was pregnant.
You could try to investigate what the below poster suggested by figuring out if low fat cheese seems any better and can you drink milk without hazard? Also I think that Feta cheese, goat rather than cow products, are easier on the stomach.
On a lighter note, you never know, if you have another child the cheese trend could be reversed. I sympathisize, life without cheese includig pizza and lasagna would really suck. At least you weren't diagnosed with arthritis in your back, which followed on the heels of my third child's birth, lol.