Weird Codeigniter behaviour.

Hello,
so i came up with two problems today. I was just editing bootstrap files when suddenly something stopped working in codeigniter, first of all when I enter any website section added by me, I see following:

File not found

I checked header in chrome, so I know it's 404, why Codeigniter 404 handling doesn't work? I still use development enviroment. Secondly it happened suddenly in my whole website, at any subpage of my website defined in routes, I see message as written above...I found temporary solution:

https://gist.github.com/philipptempel/4226750

Before I used .htaccess that way:

PHP Code:

<IfModule mod_rewrite.c>
    RewriteEngine On
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteRule ^(.*)$ index.php/$1 [L]
</IfModule> 


It is still working in live websites created by me. I really can't find a solution to this weird thing. I bet that any super advanced user of that great framework can point out what gone wrong. Please tell me what do You need to inspect that case, I will provide necessary details and informations.

Cheers. 

@edit

Ok, problem solved. Something messed up with compiled modules by server operators, everything fine now.