Probably a small difference in their framecount.
The time is determined by frame count * duration of one NES frame. They must have the exact same amount of frames.
EDIT: just played the game and I must say that I'm a little disappointed. Not only is this one of the most boring games I've ever played, there's also no skill involved at all. At least not in this level. The only time you have to use your weapon is when you have to get past the three snakes at the beginning. That's the only time you have to let go of the B button for a split second. Throughout the entire run, excepting that one part, I could just hold down right and B and never let go. I didn't even really have to practice it, I just started recording and a few tries later I had a good run. There are only like two jumps that are pretty hard, like the one right at the end where you have to jump off the last few pixels of the platform in order to catch the elevator without losing your speed.
Unless you don't know you can run by using B, I don't see how it's even possible to get a time of over 1 minute.