You don't need to ever defrag your OS X drive. Leave it be and it'll treat you well. Get into optimizing, and you're just wasting time. Fragmentation, unless it's caused by some problem with your system, won't cause you any problems -- in fact, it's perfectly normal for a UNIX-based system, and Mac OS X will take care of most of the optimizing/defragmenting for you automatically.
And, please answer bobw's questions -- it would be very helpful to know what software it is exactly... system update, 3rd party program, etc.