In case we activate URE for single site it reads options from the site for which it is activated, not from the primary blog.
And ‘Yes’ I should re-test what is happend now with network wide settings from the ‘Multisite’ tab. It may stop working.

Other problem you showed to me – the “Multisite” tab of single site activated URE plugin should be available to the super-admin only. I will hide it from other administrators.

Try this hack as a quick workaround to provide single site administrators access to the URE: add this line to the wp-config.php