Download Calibre and then add the books into that program. Attach the Kobo reader. Calibre should recognize both the reader and the card. Highlight/choose the book you want to transfer and click on the menu to the right of send to device. Choose to send to the card. Does it transfer that way? I'm suggesting this because I am not sure if the way you are trying to copy is part of the problem.
The updating content bit is normal. Your Kobo has to check to see if there is new content to process, bookmarks to sync, etc. It is very fast if there really isn't anything, but can take a long time if you, for example, have just popped in an SD card with 100 books on it.