You have picked a really great project from the Science Buddies website.http://www.sciencebuddies.org/science-f ... background
The project guide specifies isopropanol, which is a polar solvent. Acetone is less polar. One of these solvents should be suitable for solubilizing the plant pigments, which you are trying to separate.
Here are some suggestions and questions to answer that may help solve the problem.
1. Have you tried a different brand of paper towels?
2. Did you concentrate your sample before applying it to the paper towels?
3. Try covering the Mason jar to saturate the atmosphere in the jar with the solvent
4. Have you tried 100% acetone?
5. What types of leaves are you working with?
6. The procedure in the experiment is very detailed. Can you confirm that you followed every step? Did you vary any of the steps at all?
7. Applying a very concentrated spot of the plant pigment at the origin is very important for success. Was the starting color spot a very intense color? If not, try applying lots more pigment.
Please post again if you don’t see separation of the pigment colors with answers to the questions. You definitely do not need to change projects.