Can CodeIgniter change .htaccess all by itself?

[eluser]CroNiX[/eluser]
Not sure what else to suggest. Things don't just change themselves, and if you or your app isn't doing it...

One thing that's also strange about the htaccess you first posted is this line is commented out:
#RewriteCond %{REQUEST_FILENAME} !-d
and it shouldn't be

You can also get rid of this:
RewriteCond $1 !^(index\.php|images|robots\.txt)