From what I understand it has to do with gears meshing together. If they aren't lined up properly it simply won't go. You can try the double clutch method like some people mentioned or you can roll the bike forwards or backwards to spin the gears a little and then they line up. My 08 Busa did this for a little while, I'm at 1,800 miles and it hasen't happened. So the explanation someone gave about rounding out the edges (I'm paraphrazing) makes perfect sense.
By the way, I'm new hear and love the site, thanks for having me. I'll post pics of my Busa shortly, I suck with computers so I need my wife to post them for me.