ITÃÂ´S A MAYOR ISSUE OF THE MAGENTO PLATFORM.
The problem comes about because Magento Backup sets permissions on files.
The offending piece of work is lib/Mage/Archive/Helper/File.php
In it you find a function public function open($mode = \\\\\\\\\\\\\\\’w+\\\\\\\\\\\\\\\’, $chmod = 0666)
This causes issues where permissions are changed globally.
If you must use Magento\\\\\\\’s site crippling backup, then you must run a script to set the file/folder permissions back.
Magento file permissions 500 error
Reseting file permmissions