The problem :

when i used several 'choosecoursefile' element with an array of it, the return key of the value is for example :
file[0]
file[1]

and not an array of file.

The solution :
The problem is in the 'MoodleQuickForm_choosecoursefile' class with the function 'exportValue' (file : \lib\form\choosecoursefile.php).

The original code is :
#
function exportValue(&$submitValues, $assoc = false)
{
    $value = null;
    $valuearray = $this->_elements[0]->exportValue($submitValues[$this->getName()], true);
    $value[$this->getName()]=$valuearray['value'];
     return $value;
 }
#

I proposed this modification wich works fine
#
    function exportValue(&$submitValues, $assoc = false)
    {
        $value = null;
        $valuearray = $this->_elements[0]->exportValue($submitValues[$this->getName()], true);

$name = $this->getName();
if (!strpos($name, '[')) {
$value[$this->getName()]=$valuearray['value'];
return $value;
} else {
$valueAry = array();
$myIndex = "['" . str_replace(array(']', '['), array('', "']['"), $name) . "']";
eval("\$valueAry$myIndex = \$valuearray['value'];");
return $valueAry;
}
    }
#