What do you mean by "when I scan my game folder"? Do you mean "I only get media for 5 games" or "there's only 5 games listed in the main list"?
If the reply is "I only get 5 games listed" the reason might be:
- the original files are not in the proper file format (allowed extensions for Dreamcast are: .cdi,.chd,.gdi
- there's a filter applied on your list: filter on favorite, keyword, players, ...