Yes. She flunked her engineering ORI's in February, 2003, just before the Iraq War, when she failed to get boiler pressure from a cold light-off within the allotted time. Her skipper and engineering officer were relieved immediately. (Not that other people didn't deserve a reprimand as well, up and down the chain of command -- and get one.)
Sometimes it takes people getting their careers dinged pretty badly, before an old ship can get what she needs.
Elsewhere on FR, it was discussed in another thread that the John F. Kennedy is in tough shape, unable to use two of her catapults and therefore effectively reduced to flying a few Harriers and helos off her decks. She's pulling some kind of scrub duty from an East Coast port -- training duty or something -- and is in very bad physical condition.
It might have been the same thread, but the JFK has had her arresting gear de-certified, too. So she is effectively a very big LHA/LHD, unable to launch or recover fixed wing aircraft.