If you load in a Plugin after Server start, like this:

Plugin pl = Bukkit.getPluginManager().loadPlugin(new File("/path/to/your/plugin.jar"));
Bukkit.getPluginManager().enablePlugin(pl);

commands will be loaded in but Tab Completion will not be available for those Commands and it will appear as if those Commands don't exist to the player.

 
To recreate this behavior, i have attached 2 plugins. Place 'Bug.jar' normally in the plugins folder and Bug2.jar just in the Server folder, Bug2.jar will load but command tab-completion will be unavailable (even though the plugin will be listed in /pl). Now use /bug and you will see that it will output '/bug'.