I had this problem on a unibody MacBook. The solution was installing the 10.6.2 combo update.

The replacement upper case cracks aren't harmful to the computer, however, they look worse than a mouth full of missing teeth. My suggestion to you, is to call Apple and ask them for a replacement. There is a somewhat unknown replacement program for the case chips and cracks. Alternatively, you could always buy the case part from ifixit. ;-)