That's normal for BaseCamp, it doesn't actually show all of the folders on the Etrex. And its only lists maps on the Etrex if they are specifically set as visible for Basecamp.
If you look in My Computer, you can see what files and folders are actually on the Etrex. Though it doesn't really matter anyway, you can just use Basecamp for loading everything, and it will put it in the right place.