Forum index.php - does not contain expected contents

[محروم.كوم]

Hi, it looks like my site was abused. I noticed an "alien" code in footer, which I deleted. I got the latest version vBulletin 4.2.0 Patch Level 3, uploaded all new files to my server and upgraded my forum. Now when I diagnostics -> Suspect File Versions I see that:
- index.php File does not contain expected contents;
- forum.php File not recognized as part of vBulletin.

I uploaded the new files several times but it didn't change anything. I checked that only the plugins written by me is active and the code is original (written by me).

Please help me to understand what does it mean and how to fix it? Thanks in advance. __DEFINE_LIKE_SHARE__