Commands, plugins, all stopped working a while ago

I'm not sure what it was, but we had monsters off when it was hMod (This server is being run through artofwarcentral.com, mind you), and when we turned them on and messed with some other things in server.properties, all of our commands stopped working. We turned them on while it was in craftbukkit, and the settings didn't work right, but it did turn on the monsters.

*Am I not supposed to use server.properties anymore?*

It won't let us access any commands, or plugins. I've been fighting with it for a week or so. You're our final hope.

EDIT: It's running craftbukkit 0.0.1, is this the latest version?

 

CraftBukkit 0.0.1 says nothing, as all the builds are currently version 0.0.1, as there's been no official release. This is where they're listing all the CraftBukkit builds. The most recent one that I've personally tested on my server is build 141. Try updating to that one and restart your server, see if you can use the plugins and commands at that point.

Also note, CraftBukkit, unlike hMod, has NO built-in commands at this point. If you run CraftBukkit with no plugins (nothing in the plugins folder), you're basically running a vanilla, almost-Notchian server.