The Kunena team has announce the arrival of Kunena 6.2.5 [K 6.2.5] which is now available for download as a native Joomla extension for J! 4.3.x/4.4.x/5.0.x. This version addresses most of the issues that were discovered in K 6.1 / K 6.2 and issues discovered during the last development stages of K 6.2
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tl;dr
I have a VPS and the index.php's where getting compromised.
Was advised to delete files and keep configuration.php and reinstall components / plugins.
All my Joomla plugins/components have re installed fined except Kunena.
I downloaded the zip and extracted from here, all installed except com_kunena.
I am using the latest Joomla, latest Kunena and PHP 5.3.29
save the configuration.php file and your images and personal files one by one, (not the folder as it may contain unwanted files)
wipe the entire folder where Joomla! is installed
upload a new clean full package latest version of joomla 1.5.x or Joomla 2.5.x, joomla 3.x (minus the install folder)[2]
reupload your configuration file & images.
reupload or reinstall the latest versions of your extensions , templates (even better is to use original clean copies to ensure that the hacker/defacer did not leave any shell script files in your site)