If you are feeding anything other than lab block I would switch to that ASAP. I had the same issues breeding rats years ago when I was feeding dog food. I tried all different brands and levels of quality, but would have random rats die. I even had a pathologist at a top ranked vet school do a necropsy to confirm the absence of transferable diseases.
In research labs we feed rats traditional lab chow and very rarely if ever have spontaneous deaths.