rootFile a NIL value

This looks like catalog corruption. Either go back to a catalog backup from before this issue started, or try this: Create a brand new catalog and the use 'File - Import from Another Catalog'. Import your old catalog. Do not move the images, just import them without moving. This should import all the images that are in your old catalog, including all their metadata, collections and other stuff. The new catalog will be an exact copy of the old one, except for one thing: The only thing that won't import is any publishing services you may have. As the empty grid cells are not actual images, they should not import either and so your problem is solved. Trash the old catalog and use this new catalog from now on.

internal error has occured: ?:0: attempt to index field 'rootFile' (a nil value)

Do you happen to hav the Logitech Options plugin installed?