Hi misternik,
i think this could be a configuration problem with your server, most hosting packages have the php_max_execution_time set to 30 seconds, and more than 500 keywords could cause this time to exceed. If you have root access to your server, then you can set this to a higher value. If you have a hosting package, then you may consider to upgrade your package, or even upgrade it to a server, since 500 keywords is quite a high number of replacements. Maybe you can post some more information about the server you're using (eg processor, php configuration details, number of domains hosted on your server etc). This would help to determine if it's a problem with sitelinkx or with your hosting package.
Maike