HI Fist off start your mac up with the Shift Key pressed and keep it pressed till the mac completely starts up and gets to a safe boot screen - if it dosent get to a safe boot screen then you didnt press the shift key quick enough on startup /or you are using a wireless keyboard - try one with a wire on it- once thats done (It performs a diagnostic repair automatically) run a permissions repair as before, then reboot your mac ith the OSX Disk as if you were going to re-install the OS when you get to the first / second screen of the installer window you will get a utilities menu at the top -
choose disk utility from there and run disk utility and repair the startup volume, re-boot and that should cure it, but do a softwaer update as well

Hope this Helps

David

Thanks for the reply and idea David.

It didn't change the warning issue.
I did contact Apple on this and they had me do basically the same minus booting into safe mode.

I assume, in safe mode, that the diagnostic repair you mentioned is run in the
background (not visible), as I saw nothing unusual except my 22" screen was cut in size down to about 2/3rds. By the way, I use nothing wireless.
I did do a software update before and after.

Apple says as long as it says repairs complete, not to worry. Had I talked to a tier 2 tech, I might have gotten a better explanation of what those warnings are and why they are there. But if I'm not experiencing any other problems, I won't worry anymore.

But my curiosity is still there as to what they actually mean. Need to got to Apple school.

Thanks again for a timely and informative reply,
Dan