Putting
require_once('Classes/PHPExcel.php');
inside a loop is not a good idea. It belongs at the top, above the loop. After all - it will only be opened once.
And the same goes for your function declaration! The first thing you should do is move both the require once and function out of the loop and see if it works a bit better for you.
Also, since each converted file will get the same name you'll end up with, at most, once converted file: the last one you convert.