Look on the "Files" tab for the movies that have covers that don't show up and see what the filname is in the "Covers" field. Is it the same as the names of the files you have for those movies? And are those files located in your cover folder?
If you don't know what folder your covers are stored in then look under the "Tools" menu, select "Configuration and on the "Directories" tab you'll find the path in the "Cover Directory" field.