Because, while Samus runs the number of pixels per second in both versions, the European version only gives you 50 button presses to work with every second instead of 60. The game cannot be played as exactly and time is lost troughout. That's what I remember Flatley saying earlier at least.
Edit2: So, he met a girl in his dream who gave him a large phallus that fires an unidentified white substance when he clutches it. How Freudian.
One frame here, one frame there — they all sum up pretty well, you know. There are enough microscopic mistakes (on a frame level; maybe not even mistakes but just unwise moves) in Terima's run to squeeze another couple of seconds while cleaning them up.