Phantom Folder

Phantom Folder

After upload of data some  files are appearing twice in the view "all files"; when I checkout both the files they appear in the view "Checkedout" and I can go to the related folder - in both the folders same files are visible - BUT only one folder is visible in the folder tree.
 
So one can navigate to the duplicate folder through the checkedout view folder link - but that folder is not visible in the folder Tree - This is not a one of case - I have already identified 2 such cases.
 
Please look into this urgently.
 
Rajesh