Hi,
Are you using build 418? If not, try updating.
Beyond that, it's hard to say what's going on without more info. This isn't a known issue. As you can see from the questions I was asking previously in this thread, we need some details to figure out what's going on.
If you logged into Windows with a different account, this might happen.
If the files in the collection folder got renamed so they don't have the correct file extension, this could happen.
What files are in which folder? What were the missing collections called?
Greg