Here's a newer article with better details.
http://www.boston.com/sports/footbal...ls_for_af.html
The key part about the problem being fixed at halftime.
"ESPN Sports Radio 810 in Kansas City reported that the Patriots footballs were tested during halftme, re-inflated after when they were found to be under-inflated, then the balls put back in play for the second half and then tested again after the game."
Even disallowing all the first half points leaves the Colts down 28-7
Steve B