phpmyadmin index.php file disappeared - linux

I am having a very strange problem.
I am having a Debian machinem,
once in a while the index.php file of my phpMyAdmin disappearing, and I need to reinstall / copy it back.
I don't know what causes this weird behavior.
and I thought that maybe someone had hacked to my machine, so I had tightened my iptables rules. and set the permission on the index.php file to read only for user,group,and everyone.
And still it been deleted today.
I don't know what to do, I had googled to see if this might happend because of bug of any kind, or software update. but couldn't find any hints.
So here is my question:
1. does anyone encountered such behavior?
2. if someone hacked into my server how can I find it? (there is no unknown login in my logs, and I had checked all the IP's of the logins seems to be a valid known my IP's)
3. how can I find out what is deleting or causing this?
Thanks in advance,

it seems my machine was hacked, so I had just created a new machine with tighter security and this never occurred again up to now.

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Drupal menu items and blog entries disappeared for anonymous users

I've been struggling with a problem now for a few hour and I cannot find any answers or anyone with the same problem -
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================FIXED<<<<<<<-----------------------------
I am not allowed to answer my own question and it was suggested that I edit the question to include my answer so here goes:
Firstly, thanks for all the responses.
I disabled the "ACL" module (http://drupal.org/project/acl) and the problem was solved. It was previously used for our forum which was also disabled a few months back, so it's not needed any more.
I still have no idea why this module caused the site to work locally but not on the server. I will be in contact with the server admins to find out if they changed/updated anything on the server which may have caused this module to cause a malfunction.
Any insight could still be helpful top prevent this from happening again.
Check your Drupal config:
Are you using node_access, content_access, or any other permissions-related addon mods? Disable them and see if the problem persists. If that doesn't work, disable all non-core mods and re-enable them one-at-a-time until you find the offender.
Compare your hosting configs:
If it's not related to Drupal, compare the local and remote server configurations. Do both use the same versions of php, apache, apc, cgi, etc.? A phpinfo(); on both servers should give you the most important details for comparison. Do a similar comparison of the MySQL setup and content. Finally, check for differences in your .htaccess files (if any) between the two locations.
Test another hosting enviornment:
Download a virtual appliance like QuickStart which is already configured to host Drupal sites for development and non-production purposes, and see if the site works correctly in that. If it does, you could do an additional validation by porting to a new host who offers a trial/money-back-guarantee and see if it works correctly there.
If your site works fine elsewhere, give your current host a good thrashing for making you go through all of this to figure out the problem lies on their end.

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