Can CodeIgniter change .htaccess all by itself?

[eluser]PhilTem[/eluser]
If you wrote all of your app's code by yourself and have never written anything that changes the .htaccess-file deliberately, then you won't be changing it.
Futhermore, I really don't think that your host service changes a .htaccess file in your public_html. That would be a little weird, but maybe they do it that way. To me it would be more reasonable to have another file but .htaccess changed by your setting in the cPanel.
Assuming above mentioned thoughts, I guess, that someone else is changing content of your .htaccess file. Does anybody else have access to your server?

Maybe you want to try changing the permissions on .htaccess to 600 and see what happens (as long as you are able to and the owner is you but not the user that your host's webserver runs with)