Okay for posterity I have managed to track down a very reliable trigger for the flashing redraw in the header: the highlight action. Opening a book and highlighting some text (even if you immediately undo it) seems reliably to trigger the flashing redraw, even on the latest firmware. Exiting the book and reloading it will make the flashing stop.
That being said, I'm also seeing the flashing happen on the center of the header, where the chapter progress is displayed, so I am still very certain that there's nothing in the code of nickelclock that causes or could prevent this, but in case anyone wants to forcefully trigger it for testing purposes highlighting is very consistent. I think any action that displays one of the modal menus (where you can add a highlight, or else search a word in the dictionary, etc) will do this.
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