Are you talking about using a one-click install?
If it's telling you that the directory isn't empty, the old software probably created an .htaccess file that you're not seeing (I don't think all FTP programs show hidden files by default).
If you're not familiar with using SSH, or can't get your FTP client to show hidden files, you could just delete and re-create the empty directory that you want to use.
Example. If you have yourdomain.com/forum -- and you think that forum is empty -- just delete and re-create the forum directory... not your whole domain directory.
If you're familiar with SSH, just log in, CD to the folder, then type ls -all. That will show you everything that's in the folder, which will probably be .htaccess.
If you want to get rid of it, just type: rm .htaccess
Does that help, or did you mean something else? I'm assuming you're using the one-click-install feature in the control panel, right?
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