I came up with the idea it has something to do with the timeshift stone. Msot of us who didn't experience the problem either didn't do lanayru first or 2nd (i have done it first twice but with no issue) and probably just left after reviving him. I thought that, if you do him first, the 'objective'/requirement of that song piece is reviving lanayru. So i believe it's possible that, if you revive him and get the piece of the song, but then for some reason, hit the timeshift stone in to the present (where lanayru no longer exists) it prevents Eldin/Faron scenes from beginning.
people who complete lanayru last will not experience this issue due to the last trigger of this portion being Impa recognising the master sword.
However, if the objective of Lanayru's piece is indeed 'revive him' then the game may not recognise the piece as complete if you leave while he is dead.