have you got the original disks -- you could run the hardware test.
I had this for a long time until I realised that some time before I had
started from an external disk, which i later removed. Selecting the
start-up disk again manually (it was the only one listed) fixed it.
if you're getting funny sounds from the disk itself, I'd worry.
of course you have your regular back-ups handy just in case...?
They also say you should rebuild disk permissions after an installation
(in Disk Utility).
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