the difference is the auto reset that arduino uses, if you are using ISP to program another 328 you dont need it
http://arduino.cc/forum/index.php?action=unread;boards=2,3,4,5,67,6,7,8,9,10,11,66,12,13,15,14,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,86,87,89,1;ALL