Got the same issue with PHP 5.3.14 on openSUSE Tumbleweed. But it's not GD related.

Backtrace:

#0  zval_mark_grey (pz=<optimized out>) at /usr/src/debug/php-5.3.14/Zend/zend_gc.c:372
#1  0xb67c742d in gc_mark_roots () at /usr/src/debug/php-5.3.14/Zend/zend_gc.c:435
#2  gc_collect_cycles () at /usr/src/debug/php-5.3.14/Zend/zend_gc.c:664
#3  0xb67a63f5 in zend_deactivate () at /usr/src/debug/php-5.3.14/Zend/zend.c:901
#4  0xb6746aa9 in php_request_shutdown (dummy=0x0) at /usr/src/debug/php-5.3.14/main/main.c:1661
#5  0xb683ab44 in php_apache_request_dtor (r=<optimized out>) at /usr/src/debug/php-5.3.14/sapi/apache2handler/sapi_apache2.c:509
#6  php_handler (r=0xb6f05058) at /usr/src/debug/php-5.3.14/sapi/apache2handler/sapi_apache2.c:681

Code which crashes:

<?php
ini_set('display_errors', true);
error_reporting(E_ALL);

class Plugin
{
	private $name;

	public function __construct()
	{
		$GLOBALS['app']->getFoo()->activePlugin = $this->name;
	}
}

class Plugins
{
	private $plugin;

	public function init()
	{
		$this->plugin = new Plugin();
	}

}

class LegacyApplication
{
	private $plugins;

	function init()
	{
		$this->plugins = new Plugins;
		$this->plugins->init();
	}
}

class Foo
{
	public $activePlugin;

	private $bar = array();

	public function init()
	{
		$this->bar []= 'bar';
	}
}

class Application
{
	private $foo;

	public function main()
	{
		$GLOBALS['LegacyObject'] = new LegacyApplication;
		Application::getLegacyApplication()->init();
		$this->foo = new Foo();
		$this->foo->init();
	}

	public static function getLegacyApplication()
	{
		return $GLOBALS['LegacyObject'];
	}

	public function getFoo()
	{
		return $this->foo;
	}
}

$app = new Application();
$app->main();

echo 'OK';
?>

And now the same problem on FreeBSD 7.4-RELEASE-p9, PHP 5.3.16 with Suhosin-Patch

Don't see how it is related to GD, there is no trace of GD code in the backtrace.

I'm sorry to report late. I tested the same script on PHP 5.4.6 and don't have any problem now.
Thanks.

I've already wrote that it's not GD related.

I don't experience this issue any more so I close it now.
Thanks.