I've run into this many times myself. Here's how to fix it: Make a new .zip in your mods folder, you should name it with the name of the mod you're trying to get working, followed by "(fixed)". Open up both this new .zip and the mod you want to use. Move all .classes from the mod into the new .zip. By that, I don't mean just select EVERYTHING and move it over, I mean move over the classes you see, then go into each folder in the mod and move their contents over as well.
In short, you're unpacking all the contents of the mod so that all the files are out in the new .zip and not organized under folders. This new .zip should get recognized by magic launcher.
In short, you're unpacking all the contents of the mod so that all the files are out in the new .zip and not organized under folders. This new .zip should get recognized by magic launcher.
Cubic Chunks Suggestion! (Link in text mode because banner image is 404) Cubic Chunks Mod below: