Apple released an update for the Migration Assistant today, stating the update fixes an issue transferring data, settings and applications from a Mac running OSX Snow Leopard to a Mac running OSX Lion.
So if you are planning on upgrading to a new Mac Computer with Lion, be sure to get this update first. If not, you will likely lose your data, settings and some applications after you transfer to Lion. This is not for users who are just upgrading their current Mac computer, but for users who plan on transferring their settings and data from a Snow Leopard Machine to a new Lion Machine.
To get the new update, just check for software updates for you Mac, or visit Apples site here to download it.