One more thing…you don’t need the shader effector or the 2nd random effector. Just use the random effector you called “color effector” and on the Effector tab, set the Random Mode to “Sorted” Then all the colors show.
I deleted the texture you had on your cloner, created a texture with a multi-shader in it, gave it 6 colors, set it to index and applied it to just the body and it worked fine….
What version of Cinema are you using and on what platform? Also 32 or 64 bit?
You could try using image sequences instead of movies. There have been some problems in the latest update of Cinema with using .mov for textures on 32 bit systems.
Create a new texture
Under the Color tab, select Mograph>Multi Shader as the texture
Click on the white color swatch and add as many color shaders as you need.
In the Multi Shader, select Mode: Index Ratio
Apply texture to your cloner.
It is a photoshop question, but you can use SELECT >LOAD SELECTION and then select your alpha channel. You should then be able to cut your image. You could also check the invert box and then use the selection to delete your background…