“Show theme/plugin notices to admin only” option at URE’s option page uses WordPress built-in admin theme CSS classes to hide HTML element simply changing its ‘display’ property to ‘none’.
I think that ‘clientside’ plugin redefines notices part HTML/CSS structure. So this URE’s simple hack stopped working.
You may try more advanced technique to force WordPress do not output such notices at all. May be it will work this way for the modified admin theme.