“Warning: SUID file has been modified and will not be repaired” after repairing disk permissions

Solution 1:

It's simply telling you that the file has been modified, and because it's been modified Disk Utility can't fix the permissions on it.

ARDAgent.app is the Apple Remote Desktop agent, and the file shown in the path above is the binary file contained within the app package. It's normal for the file to be shown as an error here. Simply ignore it.

Apple KB article TS1448 details which error messages you can ignore in Disk Utility.
The error that you provided is shown in the list, so it can be safely ignored.

Disk Utility's Repair Disk Permissions messages that you can safely ignore

• Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent" has been modified and will not be repaired.

Solution 2:

Don't worry, this is one of the messages that are safe to ignore. For a full list, visit the Apple Knowledge Base article on this topic.