FRED doesn't load the mod selected in the Launcher (which ought to be changed, I think). Wherever your put the Nebulas needs to be selected in FRED's target box.
Example: say you want FRED to load the MediaVps folder. To do this: you create a shortcut to FRED and click Properties (or just click properties on an existing shortcut). In the target box, at the very end (and outside the quotation marks) put a space followed by -mod MediaVps (there is also a space between "mod" and whatever folder you're loading). FRED should now load the MediaVps folder when you use that shortcut.