You should probably consistently use one form of path, and not intermix the two.
MC stores the path information about media in a per-file field, [Filename]. It tests this field's value to determine if a file is considered missing (or the absence of an entry in the library to consider as an import candidate). Note how MC sees these file paths as different:
U:\HD Movies\Batman
\\ULTRANAS\media\My Videos\HD Movies\Batman
It also stores cover art, depending on media, relative to this file path, and the field [Image File] indicates where this cover art is located. Cover art gets cached for media in MC's library. It might be that by browsing via alternate paths that the cache lookup fails for the media, as the media isn't in MC's library (via alternate path).
Also, when using a UNC path, be sure the UNC path is writable so that cover art can be stored.