when I do the plugins command in the server command window, it shows that they are installed. but from the game it says 0 and the plugins do not work. I just switched bukkit to 1.3, and the server works fine except the plugins. Any help would be appreciated!
maybe the plugins are outdated. i had this too. If you have craftbukkit version 1.3.1, and your'e using plugins for 1.2.5, it will break. try to figure out if the plugins are outdated, or not.
All of those are updated for 1.3.1 if my memory serves right. Did they work on server start? If so, /reload broke them and you should just restart the server when you want to update plugins.