Be careful on trusting the SEF Status "Enabled / Disabled" on Control Panel - right side. They might be wrong!

In my case: I didn´t get the results I needed when editing the basic config / extension config. I lost hours of work. Reason: SEF Status "Plugin" was shown as "Enabled", I turned it off - and now Plugins (Extension configs) are parsed as expected!

GOOD LUCK!

Hi,
The problem is caused by Joomla caching the plugin status. We'll fix it in next version. In the meantime, you can control the JoomSEF's plugin status in Joomla's Plugin manager.