You are right..something could be wrong or it could be a reaction to the food.
The fastest thing you can do is either get your new cat in for a full vet exam (if you haven't yet, it is always wise to do so when you get a new cat), or at the very least, take in a stool sample to be checked for parasites.
I'd go for the vet exam - so they can check kitties breath/dental health, palpate it's belly, check if there is a temp and much more.
I fed my foster kittens IAMS Kitten, and that seemed to really give them gas.. so I bought something else, and it went away.
Vet is your best bet, the little kitty will need her shots and everything anyway. Take a fresh stool smaple and like Pat & Alix said, they will do a test for parasites and treat her for the one she may or maynot have. =)
First have the kitten checked by a vet...but we had the same problem and it was the food. The high quality kitten food he was on when we took him in was causing aweful gas...then we switched to Chicken Soup for over two months and it got no better...we then switched BACK to the food we had been feeding our cats for three years and it has pretty much gone away.
If the kitten hasn't been given the once-over by a vet, that would definitely be the first step and before anything else.
If there isn't a medical issue, then please come back and we can try to troubleshoot other things. It could very well be the food you feed her or the cat litter you use that is causing the smell to get out of hand.
But like the others said, the first thing to do is to get the kitten to the vet for an initial exam and basic checkup.