Wikimedia Bugzilla is closed!

Any extension hooks (in my case, the SyntaxHighlight.php extension) setup using
$wgParser->setHook() are parsed before template variables have had the chance to
be replaced.

In my case, this gets in the way of using the SyntaxHighlight.php hook for
highlighting code passed into a template. An example of this can be found at the
URL given:
http://ibaku.net/wiki/index.php/Code_Template_Example

The example uses the template found here:
http://ibaku.net/wiki/index.php/Template:Code

Let me know if other details are needed.