We're pretty sure it's to do with Game Center notification. In your case it probably occurred because you completed the Standard Goals when you scored 1 million. I got it earlier today when I completed the Wizard Goals. The rest of the time it has been fine.Same here on iPad 2 & iPod... Lots of lag/stuttering after scoring 1 million.
Then after the 3rd ball drained, the high score box didn't come up...