Yes, the on-time numbers are really shady. Because so much of an airline's performance is measured by their on-time percentage, they find all kinds of tricks to stretch the truth and shave minutes off the reported delay times. These numbers can significantly affect their funding, performance reviews, regulatory oversight, contracts with airports, unions, etc.
More good reading:
http://www.usatoday.com/travel/columnist/mcgee/2009-06-24-me...