It could be rats attacking the ducks if it's happening at night when the chickens are roosting up out of rodent reach. Besides Swampfox's excellent suggestion for detective work, you could also put in a wildlife cam (cheaper than I expected). In case you want it, here is an article on improving predator protection in existing coops. It's a REALLY long battle to get rid of rats, but it can be done.
Welcome to the coop! I use the Forums and Articles tabs at the top of the page to do research. You can get lost for hours. It's nice to know you are minutes away from getting help with questions and emergencies! I always check in the "What's New" section as well at the top of this page. This way I can read how I may have a similar question or help give some advice.