Did you use your install disk to run disk utility "repair disk"?
If not ...
Repair Disk and Permissions
These steps will check for, and usually repair, any corruption on your OS X boot volume
(1) Boot from your Mac OS X Install Disc 1 CD. Put CD in drive, wait for it to show up on the desktop, then go to upper left of screen under the Apple menu and choose restart. Immediately hold the "c" key down until you see the apple logo.
(2) When the Installer window opens, select Installer > Disk Utility from the Apple® menu bar.
(3) When the Disk Utility window opens, select "Macintosh HD" in the list on the left.
(4) Select the First Aid tab on the right
(5) Select the "Repair Disk" button on the lower right of the screen.
If errors are returned repeat this process 2 or 3 times untill they are gone.
If you still get errors then you will need to use a third-party disk utility to repair your Mac OS X boot volume, such as Alsoft® Disk Warrior®
(6) After Repair Disk completes, quit Disk Utility. Focus returns to Installer.
(7) Quit the Installer. When prompted select Restart.
Next:
Repair permissions: Close all files and applications on the disk you want to repair. Go to Applications/Utilities/Disk Utility and double click it. Then select "Macintosh HD" in the left panel and First Aid at the top. Then click on "Repair Permissions." It will take a few minutes.
If you cannot use your install disk for any reason ...
Starting Up in Safe Mode
http://docs.info.apple.com/article.html?artnum=107393
You may also have to clear your caches ...
Cache Out X
http://www.macupdate.com/info.php/id/9538
Cache Out X clears out the cache entries on your machine, helping you recover valuable disk space on your machine. Items removed include the caches in System, Users, and Library, along with the Internet Explorer download cache. Optionally clears the IE's history cache as well.
Important: Close all other applications before cleaning caches ....then reboot.
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