Permissions Repair Not Repairing the Permissions that it Claims

I have a server that went down, and I successfully archived everything [necessary] on the System partition using "sudo cp -R". I copied this over to a different HDD, and used the migration assistant to restore data during installation. This effectively copied everything that I needed to recover from this server.

Understandibly, I had lots of permissions errors, and attempted to repair them using Disk Utility while booted in the OS. This fixed most permission errors, but when I verified again, it pulled up more errors. Repaired permissions again, and again but Disk Utility still claimed that the same files needed to be repaired. I booted to my install drive and tried repairing permissions through Disk Utility multiple times, but it still pulls up the same errors.

Most of these errors are that the 'd' flag is missing at the beginning of the file mode for files matching: /System/RemoteManagement/AppleVNCServer.bundle/Contents/LockScreen.app/Contents /Resources/*.lproj/MainMenu.nib

Other errors are .nib files in the ARDAgent.app, but there are fewer numbers of these.

I assume it's pretty bad if a file is supposed to be a directory but isn't, so what can I do about this? We use Remote Desktop quite a bit, so any deviation in the way it works can be pretty prohibitive.

Thanks in advance