Okay. Just used the latest version, and here's what I did step by step.
1. I clicked the underlined 4.2.12.0 link and downloaded the file.
2. The file immediately started the download, stragely...
3. I zipped the files into a single folder
4. I open the file, and check the version. It displays 4.2.12.0, letting me know it is still the latest version.
5. I made the Starter Mod, changing all of the Pokemon to be one evolution higher than they'd normally be, unless the pokemon just doesn't have it's evolution programmed in. Only instance of this being the case is Munchlax, at least from my experience.
6. I did all 3 save options: Save File, Save Solution, and Save All.
7. I find a file called DS Patcher in the folder where I extracted the Editor.
8. I patch the Source Rom. The GUI of the Patcher makes it look like it would make the Source Rom's mods take effect.
9. I run the file using DeSmuMe manually.
10. I get Shinx instead of Luxio.
Am I missing something???