I haven't used Azureus in a while, but when you open the .torrent file, Azureus should either [1] ask you where you want to store the files, or [2] store them in a default location. Make sure you select the appropriate target directory so Azureus knows you're a seeder instead of leecher.
If you specify the target directory for the .torrent file as different from the actual location of those files, Azureus will think you're a leecher, not a seeder. In other words: your target directory should be either the directory in which your current FLAC / SHN files reside for the .torrent, OR the parent directory.