Oddly enough this happened to me yesterday for a short time. I had Calibre open with a specific search showing only one author, plugged in my reader and the reader page had the double height for the book list. Unplugged the reader, and next time I plugged it in, column height was back to normal. I thought maybe connecting the reader while a search was active was the cause, but I sure can't get it to duplicate the double height repeating the steps exactly.
Btw, this only happens under the device view, it's never happened for the library view for me.