First off, it’s against TOS to use DreamHost servers as backup disks.
I see that you used Automator, but what mechanism did you use to create the directories? Was the drive AFP mounted? When you use Transmit to examine the directory, does it show you as the owner? Did you log in as the owner, or as another user?
There’s always the option to log in via shell and do the command:
/bin/rm -rf BADDIRECTORY
This will forcefully and recursively delete that directory and everything under it. If all else fails, you may have to ask Support to fix the permissions and/or ownership.