Just watch. This is actually really good news. It means that when a sprite is cloned, each clone has its own variables. This test allows for my current project "Elements" at http://scratch.mit.edu/projects/12470185/
Basically, each clone of the one sprite is told to switch to costume # <variable>. Then, if it touches another clone's color, it changes the variable. Solid proof. Clones of sprites have clones of variables built in. If they didn't, you would see all of the dots changing color at the same time. I'm hoping to use this idea in my upcoming project. This project was my test to see if it could be done.