What image version is installed on the cRIO? You should not be seeing that message if the cRIO was imaged with last year's image.
The ni-rt.ini is stored on the cRIOs file system. You can access it by ftping to 10.xx.xx.2 (fill in the x's with your team number).
The NI Update service is what labels patches as critical. It does not update the FRC Tools, however. Make sure you've installed all the updates here:
http://wpilib.screenstepslive.com/s/...w-for-frc-2013