I recently reimported my library using the "Add books from directories (One book per directory) option. I would have expected Calibre to use the "preferred import format order" when choosing which version to grab the metadata from, for ones where I have both LIT files and ePub. But it didn't - ePub should've been prioritized first, but it used the LIT file.
It's not the newest file, either - for another book it correctly chose ePub from among ePub, PDF, PMLZ, and PRC. And it's not alphabetical. So frankly, I'm stumped.
Unless it's the order the files were added to the directory...? That could explain the differences, but if so... well, it's silly.