You might be right. You have to go back to 1999-2000 to find the last time a runner-up won the championship the next year (Bobby Labonte, 2nd in points in '99, Champion in '00).
2001 Tony Stewart finished 2nd to Gordon and went on to win the championship in '02.
But outside of that the runner up jinx has gotten worse with time.
From 2003-2012 the runner has failed to produced any type of consistency he showed the last.
2002 Runner up Mark Martin ended up 2003 17th in points with 0 wins
2005 Runner up Greg Biffle ended up 2006 13th outside the chase
2007 Runner up Jeff Gordon ended up 2008 winless
2008 Runner up Carl Edwards ended up 2009 11th and winless
2009 Runner up Mark Martin ended up 2010 13th and winless
2010 Runner up Denny Hamlin ended up 2011 9th barely scraping off a win
2011 Runner up Carl Edwards ended up 2012 15th with no wins
2012 Runner up Clint Bowyer is currently 7th with no wins
Only guy immune to suckage is of course Jimmie Jonhson who finished second in points in both 2003 and 2004.
That's alot of misfortune. lol