Sorry - I read too fast - you did say you repaired permissions. Any corrupted pref files? Drive Genius 3 is a piece of software several Mac specialists I talk with rave about. http://eshop.macsales.com/item/Prosoft%20Engineering/59100/
tells you all about it. Using one or the other is advice I received from one of the specialists I talk with. He advised me that using both (repair using one, then the other) can create a mess in my computer. So I took his word for it. :-) I have DG3 installed and it warns me when there is trouble - infrequent, but periodically it wants me to trash an arcane preference file that I need to go into "Terminal" to ferret-out. Quite impressive.