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Try booting in Single User Mode and doing a repair from there: restart and hold command + S till you see black screen with white text/type fsck -fy/type reboot when process finishes. This does a system level check and permissions repair; might fix your woes.
Next I'd try a permissions and disk repair (both) from your system install disk 1 (OS X disk). Reboot by puttiing the disk in the drive, restarting, and holding the C key down till the disk boot up completes.
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