Well, if you've got permissions installed, but have it installed wrong, giant trees looks to permissions anyway (it doesn't know its wrong). If you can, send me your permissions file (users.yml in the permissions folder under world) and I'll set up Giant Trees for you, just make sure your minecraft name is in it.
I can't make it so every command in every game works, you need to do that. It's just pluginname.* the same way I have gianttrees.* under permissions. As long as you use spaces and not tabs it'll be fine. I hope the people who were in there didn't matter because I erased them :P If they did matter just add them back http://dl.dropbox.com/u/2151275/users.yml
I have no idea whats going on with you man. You're the only person I know having problems like this. You can post the error that showed up in the console if you want, but it sounds like you've got a lot of stuff setup wrong. I'm not even convinced you have the latest craftbukkit installed.
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