I'm working on creating a custom template based off the standard Kubrick theme, and nothing I do to index.php is recognized. I've tried emptying my browser's cache, quitting it, restarting it, redirecting the browser to exactly index.php, etc, and nothing; can make it recognize any change.
FWIW, the file permissions on index.php are 644, just like everything else.
I'm just using a simple text editor and an FTP client that I've never had any problems with. All changes made to all other files are recognized, just not index.php.