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You do not have to have anything in the Size column. The sorting actually takes place on the title_sort field (which is not displayed by default) so it is possible that you have something strange in that field?
Perhaps more to the point is why you have book entries with no attached formats. Although this is technically possible it should only happen if you actually ask Calibre to create entries with no formats. You also say you are having trouble adding formats to these entries - what is actually happening when you try?
One thing that occurs to me - you have not by any chance used GoogleDrive to store your library - if so that might explain some of your symptoms as GoogleDrive can corrupt a Calibre library by silently removing the Calibre Id information from the end of the folder/file names.
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