I have my test rule setup as seen in the attached image. I am not sure what is managing your PVP zones, but this is a manual example. I can spawn a player and a chicken, both of which can be killed inside that zone.
It is possible to have multiple instances in the database for each ruleset. That shouldn't happen, but the best way to be sure is to delete the database file, reload the plugin, and reconfigure your options. Worth trying as a last resort, and of course you can save the file rather than delete if you have to go back for some reason.