I don't know how or why it would be doing this if you have them in separate folders on your computer and are importing them one platform at a time. Dump Naomi files in, tell the importer the platform is Naomi. Dump Atomiswave files in, tell the importer the platform is Atomiswave. You're either making it more complicated than it needs to be or conveying it in a way that makes it sound more complicated than it needs to be.
All Launchbox is is a visually appealing, organized collection of Windows shortcuts that may or may not have special parameters injected into the command line. That's it. It will only do what you tell it to do. If you import games that are Atomiswave games and you tell it they're Naomi games, it's not going to know otherwise, correct it for you or change it. When you do an import, the files you give it need to be for whatever platform you indicate. If they're mixed together, Launchbox isn't going to know that.