The miscellaneous files window shows all files saved in the Miscellaneous Directory as stated in the Resource Directories. It is also shown on top of the window. 

The files that are checked indicate those are already used in the Catalogue and can be uploaded in the publish tab, under the local files section.

When the file(s) is highlighted in red, that means it is no longer reachable. It could happen when the miscellaneous directory has been changed since the file was added or could be it has been removed from the directory.