I have had the same issue. Im on a MacPro with 4 disks. Lion refused to upgrade/install on the "Mac" startup disk, allowing me only to select a disk dedicated to my Fusion "Windows" files. Then when I re-started to Lion NOTHING carried over.
No .Me account information, mail, contacts, bookmarks, applications, media, documents, folders PLUS I can not "see" and of the three other drives on my desktop to access those disks -- its like they aren't there.
I was able to go into system preferences and change the startup disk to my 10.6 Mac disk (which I am working from right now). The problem is somehow in the conversion my .Me account got junked up and my calendar is off (and Lord knows what else that I have not discovered.
I have to say this is the first time I have truly been disappointed with an Apple product or experience. I can't believe that they released this upgrade without adequate testing. This is acctually worse than a Windows install/upgrade.
I have an appointment tomorrow -- I am praying that their CS reps are knowledgeable and fluent English speakers.