class.upload.php is a powerful and mature PHP class to manage uploaded files, and manipulate images in many ways. The script is available under a GPL license.
more info about the class
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But I solved my own problem anyway, instead of letting class.upload to create new directories, I rewrote it, so the FTP connection creates them.
Thank you for your quick reply.
Si posteas tu solución te lo agradecería, yo tengo el mismo problema.