Currently there seems to be a severe problem in the new plugin repository. When updating plugins from IDEA 5.x the plugin repository offers updates for IDEA 6 too. Downloading them has fatal consequences.
As I uploaded a new version of the JBoss plugin this morning, all IDEA 5.x users get an update notification. DON'T UPDATE IT. The JBoss plugin will vanish, your settings will be lost, and your plugin directory will be messed up.
This is NOT a problem of the JBoss plugin, but of the plugin repository. Currently I can't say which other plugins are affected.
JetBrains: Please fix this ASAP!