Originally Posted by Pete-KT

Our server got hacked and the code has already been removed, were working with the host now to see how they got the code into our server as it was NOT through ftp, i went through and manually removed the code and also the host is running a script to check all files.

The .js was an old exit script we had there empty files now so thats not the problem the problem was the garbage looking code at the bottom

This has been solved since yesterday morning, if you would of checked the sites before making the post you would of seen that they are already fixed.

AGAIN

I appoligize and this was only on the index pages which affiliate traffic bypasses the warning page, so no affiliate traffic was affected.