If you don't actually open your newly loaded books, they will slink off to "books" next time you sync or attach your USB to do something like work with Calibre (manage). You need to open the book to create a bookmark to keep it in "I'm Reading".
My experience has been that for folks who sideload using Calibre, or even ADE, syncing with the desktop application can add complications unless you do some careful prep work first. For example, if you started with a brand new account and sideloaded all of your purchases via ADE or Calibre, updating the desktop application and syncing or just syncing via the desktop application will result in putting that whole mess of books onto your reader in kepub format.
To avoid adding in duplicate titles, but in another format, you need to update your library via the desktop application, then rt click on the covers to remove them from the application. Sync away, and only the books that still appear on the shelves of your desktop application will be transferred to your Kobo (in I'm Reading).
Rt. clicking and removing books from the desktop application will remove the same kepub formatted books from your reader on your next sync--but you knew that already