I know how to get around it. Open up the console and type in "enableplayercontrols" sans quotes right when you go back in time (preferably somewhere in the middle of them fighting the first dragon, but far far before they say Alduin approaches), and just move around a bit until Alduin is supposed to show and just keep moving. He'll show up eventually.
I ran into this bug myself (which consistently didn't fix itself through reloading) and I managed to get it to work that way.
Lock On: Flaming Cliffs 2. Lets revitalize this game eh? http://www.youtube.com/watch?v=6FUge6ghaIo&hd=1
I can't really remember where i saw this but it worked for me. Use the scroll anywhere, wait 24 hours, talk with Partmax (or however the guy is called) but don't use the scroll on the rift, fast travel to solitude, use the scroll again and wait another 24 hours, then go to the rift of the time and finally use the scroll.