Codeigniter 3 broken - only on linux works on windows

Hi,
I've setup my Codeigniter Project on Linux, then set it up to run in localhost on Windows (XAMP). I changed some code (also tried reverting it) and did something I cant specify what.

Now my codeigniter project works on localhost but when I upload the exact same files to my Ubuntu-Server and call index.php it always shows the 404page. When I run die index.php from CLI it tells me

ERROR: Not Found The controller/method pair you requested was not found.

I don't know whats going on where. The apache error log doesn't say anything. I deleted the .htaccess files on the server. Still no result.

Any ideas?