When I compare, one window shows more lines than the other, and the font sizes are different, too. I attached a screenshot: The left window shows 33 lines, the right one 30.
To rule out some first guesses: The files match (showed in screenshot). "Align matches" or "ignore spaces" doesn't make a difference. Yes, I played with the style, but that also happens with plain vanilla fresh npp.
This is npp v6.1.2 unicode on Win XP. (But I know this effect for a couple of versions now.)