mod_rewrite enabled but Permalinks show index.php

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The output of $_SERVER[‘SERVER_SOFTWARE’] is WebServerX

That looks like your problem – check out this line in wp-includes/vars.php:

/**
 * Whether the server software is Apache or something else
 * @global bool $is_apache
 */
$is_apache = (strpos($_SERVER['SERVER_SOFTWARE'], 'Apache') !== false || strpos($_SERVER['SERVER_SOFTWARE'], 'LiteSpeed') !== false);

I think you’ll need to override this variable manually, either in a plugin or your theme’s functions.php:

global $is_apache;
$is_apache = true;

Props to @John P Bloch:

The only time it’ll automatically add ‘index.php’ to a permalink is if $is_apache returns false.

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