There are a few thing you can do to help your situation. The first is to CHMOD your files after upload.
After this: (line 246)
PHP Code:
If(move_uploaded_file($_FILES['file']['tmp_name'][$i],$folder.$file_name[$i].".".$file_ext[$i])) {
ADD This:
PHP Code:
@chmod($folder.$file_name[$i].".".$file_ext[$i], 0755);
If that does not solve your issue you may want to play around with the chown function.
http://php.net/manual/en/function.chown.php but I've personally never had to use it. It would work the same way as chmod, you'd add it below your chmod function. Example:
PHP Code:
If(move_uploaded_file($_FILES['file']['tmp_name'][$i],$folder.$file_name[$i].".".$file_ext[$i])) {
chmod($folder.$file_name[$i].".".$file_ext[$i], 0755);
chown($folder.$file_name[$i].".".$file_ext[$i], "YOUR_LINUX_USER_NAME")