Error Messages After Installing Leopard 2

After installing Leopard from the Install DVD, I used Software Update to update to 10.5.1, and updated QuickTime, etc. I also ran Cocktail, the Leopard edition. The Hard Drive checked out OK. When I ran Repair Permissions in Disk Utility, I got a number of error messages. One set starts like this: "Warning SUID file "System/Library/Private Frameworks/DiskManagement.framework/Versions/A/Resources/DiskManagementTool" has been modified and will not be repaired."
There are a number of messages like this. What shall I do?

Download and install this update, even though you've already updated.
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