As long as you double-check that box 4 is 6.2% of box 3 (on the actual W-2 software form ), then you should be OK and can ignore that unhelpful and useless message...
The Software had a bug in it at the end of last week that was "supposedly" fixed in the Online software...but has not yet been fixed in the Desktop software.
The "message" does not affect your tax filing in any way...