The screen on my Nikon D5100 flickers. This is not due to the highlights which have been turned off. The menu and information screens flickers as well... I also noticed that, when displaying pictures: the focus square (from live-view) stays weirdly overlaid on the screen (this does not appear in the real files). Both times it happened was after shooting in live view with A mode. It went away after leaving the camera turned off for a while. It seems that the firmwares are up to date (A 1.02, B 1.01). Do you know where it could come from ?
This is obviously not normal operation, and neither should you debug yourself. Get a Nikon technician and have him fix this.
Sounds like a definite issue with the camera there. I would advise taking it along to your local friendly camera dealer and see what they say. They may be able to send it off to Nikon on your behalf to get it repaired properly.