I can barely, BARELY see the difference left by that black bar after I've opened a book, but it is there on my K3. I have to open a book to a page that happens to have a big blank paragraph break at the same spot, it's impossible to pick out amongst any text.
It is possible that your unit has bad calibration data for its screen. I read somewhere that every screen is a little bit unique, and the display controller has to be programmed for the differences. If the teeny ink capsules in this batch are a little larger than the last one, it takes longer for the titanium dioxide flecks to swim across.
The data sheet for the first Epson e-ink controller google result is
Here (may not actually be the Kindle's). The external "waveform flash" chip makes me think that the reader has to have a setting for every last pixel, or they'd just put a single setting inside the controller. The thermometer sensor is interesting, the e-ink must get a bit thicker when it's cold. One other fun point, the controller gets its own video memory, so it can diff between screens. It might use that to also preload the next book page, so the CPU doesn't always have to be woken up for a redraw.