Almost all of the books on my reader, except for the preloads, are DRM free ePUB, sideloaded through Calibre. I'm hearing that drag'n'drop is not working as reliably. you do have to have the books in the root directory, and I notice that Calibre has the files themselves inside of folders (which in Calibre world have the author's name as the file name).
It may be worth duplicating that scheme with the drag'n'drop files. I'll be interested to see how this goes for you.