Glad you got it sorted.
Here is a bit of explanation for those that come along later. The order of "formats" (book types/extensions) in CC Settings is important. For each book being downloaded CC/calibre go down the list in order looking for a format in calibre's database. It downloads the first match it finds. For example, if the order of the list is (MOBI, EPUB, ...) and some book in the calibre database has both MOBI and EPUB formats, CC/calibre will download the MOBI one. If you change the order to (EPUB, MOBI) then CC/calibre will download the EPUB. If the list order is (MOBI, EPUB) and there isn't a MOBI but there is an EPUB, CC/calibre will download the EPUB.