Yeah, something's jacked up, looking into it now.
Update: Not 100% on this, but I think it's due to an issue with the world itself. I'm in the process of rolling back to a save from yesterday to see if that resolves the issue.
I still have a copy of the most up-to-date world, so if this isn't the issue I will be able to go back, but at this point, if it does fix the problem, expect that you will have a significant amount of whatever you built yesterday missing.
I've also removed all admin/mod/ops privileges for now. It's temporary.
Before taking this step, I uninstalled/reinstalled Java, deleted the entire Minecraft server directory except for the world file and reinstalled everything, and the problem remained. The last option at this point that I can see if to roll back the world.
I'll post any updates as I have them.