How many breeding pairs do you have among your pigeons, or are they all paired? If one baby of a clutch had retarded growth and died while the other survived, that would be pretty much a sure sign of paratyphoid. All the babies from all your pairs could still be paratyphoid - that'd be one guess, like the others - but by no means sure. If you know of a vet who treats pigeons, or at least is familiar with birds, or you are a member of a club, may be worth checking with either to see about getting dropping analysed from say a couple of the parent birds to check for salmonella in case they are acting as carriers and passing it to the babies when feeding. Like has been said, best check the environment they're in and maybe look at some good disinfectable flooring.
John