Welcome to the ranks of those who have been presented with a tick in a checkbox that they did not choose to make. As you found, it can take up to two hours to restore permissions to a drive that has surreptitiously grown an 'Ignore ownership on this volume' checkmark. It is the default state of external drives, which a target disk in TDM becomes. It can happen during restores from disk images, too, as I found when I used SuperDuper!, so be on your guard. Good that you found your problem and its solution, and that you triumphed.

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