Fix Joomla admin Login

Recently one of my clients sites deveoped some strange behaviour with hundreds of lines of code appearing all over the homepage etc. As a thought that it may have been hacked I tried to access the administrator section and the passwords were not accepted anymore. I checked the super admin login in PHP MyAdmin and they were not effected, but for some reason I cant login anymore. I think it may be something to do with the jos_extensions module as it seems to be missing.
Ive since deleted the site from the live server with the thought I would restore from an Akeeba backup but when I set it up on a Localhost WAMP I get the same problem which is VERY weird. Im now at my wits end and To rebuild this site would be a lot of work so im needing it sorted.
Its probably an easy fix for someone with the knowledge.